Very good points made by both of you, but there are a few things I need to point out. Your input is proving useful and I feel by weaving our ideas together, we are on the right track to creating a new plausible theory based soley on in-game canon. I will repsond with notes addressing points made in your quotes, and later update the theory with the new ideas weaved in as the discussion develops.
Anyway, the complete reply of one of the members of my Discord server (translated) follows:
I think the problem with this theory is that it is considering that the split caused by lavos falling on the planet and not falling on the planet is the same type of split that exists between home and another which does not seem to be since the reptites' timeline comes from a parallel universe whose existence does not depend on timetravel of any kind which differs from the split of keystone-1 to keystone-2 (names of the timeline in the image above) since keystone-2 only exists because of the timecrash.
Another observation in this theory is that Radical Dreamers events are observed in chronopolis as if Radical Dreamers were a parallel reality whose existence would be independent of Cross's universe.
What really gets me stuck with this theory is that I don't think that the split existing by a time travel results in two real and distinct temporal existences, the new timeline exists in the real universe while the old one is sent to Zurvan, despite the Chrono Cross restore the balance between the timelines I can't see how he would play all possible Zurvan timelines, which are imaginary, in one, so I always considered Home and Another two real timelines interconnected because of the kid project and not that one exists for cause of a split caused by a simple time travel.
-> I suppose the real timeline of the reptites could exist in the ideal timeline because of Chrono Cross since it is a real timeline and not imaginary but I discard this line of thought in favor of the real timelines that are unified are just the home ones and another since "angelus errare" interconnects only these two timelines directly and Chrono Cross is used at that specific point as designated by the kid project.
Basically
1 - Anything that exists in Zurvan is not part of the ideal timeline.
2 - Only the real timelines of Home and Another unify because of "Angelus Errare" and no other.
Ah right, what happens is that when we go to the past we mess up with the events giving Azala an advantage to win the war which makes Crono & co necessary to maintain the timeline in which Azala’s descendants are destroyed by Lavos. I simply assumed that Dinopolis came from a different timeline where Lavos never fell to the ground. Considering the end of Trigger 'Dino Age', it is observed that 'Crono' is a reptile and exists in a world very similar to the original timeline, while Cross’s reptiles supposedly evolved differently and more integrated with the planet , so much so that the technology of the elements they use is quite different from human technologies. Since the repeats of 'Dino Age' seem too similar to the way humans evolved in the original timeline, I simply assumed that Dinopolis is from a different timeline, but I suppose it is possible for 'Dino Age' to lead to the creation of Dinopolis eventually.
Theoretically, Lavos needs to exist in the ideal timeline, only he is defeated in 1999 before everything is destroyed, it needs to exist because Zeal theoretically would have existed magic is something inherent in the way that humanity evolved with Lavos' assistance.
Zurvan = Sea of dreams, is mentioned in the perfect end of Cross and Masato Kato mentioned it in an interview once (Link).
When I differentiate between real timeline and imaginary timeline I am making use of Zurvan. Real timeline is everything that exists in the universe in a material way while all the possibilities of timelines exist in Zurvan in an abstract way, in zurvan there are all dreams, imaginations, thoughts, ideas. When Lucca wonders at the end of the trigger about what happens to the timeline that is no longer allowed to exist, at the perfect end of the Cross, Kid says that they will return to Zurvan the sea of dreams. So in the DS Trigger they give the name of the merger of Sara and Lavos of Dream Devourer, existing materially in a place that he shouldn’t exist he started to feed on Zurvan’s dreams, within the dreams the denied timelines, only that any real timeline that exists from a change it is always dependent on a denied timeline, as if there was a kind of "quantum entanglement" (for lack of a better word) between them, eventually devouring the timelines denied in Zurvan, Dream Devourer begins to devour time itself by becoming Time Devourer.
- On the notion that Lavos himself could not have caused the split, I can agree to this. However there is another more plausible option that makes more sense and leaves the premise of the theory the same. Lavos falls to earth and the events of CT unfold as we know. As I said before, when history is changed new timelines are created, seeing how it is stated in Cross that there are as many timelines as there are possibilities it is safe to assume that there are more unknown realities aside from the 5 timelines that are directly confirmed in the games. With that in mind, I cannot get behind altered timelines simply going to Zurvan rather than there just being a split based on both possible outcomes. As I said in my last post, the refrence of everyone being dreams of the planet dreaming the dream of life and that all dreams eventually return to Zurvan more than likely points to where lifeforms go when they pass.
But I digress, the main issue here is what causes the Dinopolis Timeline. It is stated in Cross that Lavos in Antiquity could sense that it would be defeated in the future and pulled Chronopolis from the future that it was defeated to that period. This was due to their use of the Frozen Flame (a shard of Lavos) during the Time Crash incident. Then the Entity (planet) pulls Dinopolis from the future of a timeline where Lavos never crashes into the earth to counter it. So what I am thinking is that upon seeing what happens with Chronopolis, the entity itself splits the timeline before Lavos comes to the planet to allow Dinopolis to exist in the first place. It was an action of self defense afterall.
- I would not take to seriously anything found in the New Game Plus endings as absolute canon. For one, the ones in CT were made long before Cross was a thought. And more importantly, they are not made to be taken seriously as the contradict the main plot itself. An example of this is that in the General Kid ending, the Dragon Tear is now the Frozen Flame. But the item in hand is still the Dragon Tear from the main game. Also in Trigger we know of Time Traveler's Immunity, yet in one ending Marle is made to be a Frog. So I would not put too much stock into the Dino Age Plus ending and the tech being the same as the humans.
A more accurate comparison would be the Lost Sanctum in the DS release and beyond. The Reptites here are clearly more in tune with nature than their human counterparts in the same time period.
- The Radical Dreamers timeline is likely a split that takes place before Cross, and exists alongside the two we play in. It actually makes sense that FATE would be watching it, because if its plans failed (and FATE did not die) it was another world it could make contact with the Frozen Flame. Also remember that FATE could not direcrly influence Home World either, so the fact that the RD timeline was only being observed at the time does not mean it is any less of a split than Home World was. It just was not a split that any of the characters in Cross were directly involved with.
- Kid never says deleted timelines go to Zurvan, Schala/Kid say ALL dreams go to Zurvan eventually. This is right after calling all lifeforms themselves "dreams of the planet", which makes it seem more like an afterlife reference where souls go when they die.
- I cannot get behind the idea of only two timelines being merged, because there are 3 in total that actually show us interaction within Cross itself, even if you ignore the RD timeline entirely. The Dinopolis Timeline is present and shows influence throughout the entire game. It has become part of El Nido itself and if a merge of the two were to take place, Dinopolis by default would HAVE to be included. The Dinopolis Timeline still has Terra Tower hurled back in time, but without a merge it has nowhere to go. One could argue that the Chrono Cross heals that timeline as well, and Terra Tower simply remains untouched by the entity as there would no longer be a need to throw it back in time, but that would show influence beyond the two timelines we play in, which is my point. I also do not see Zurvan being an option here, as Dinopolis would have already been written out by the logic within the quote. So with that in mind, it is evident that more timelines are affected by the Chrono Cross than what we see. It is completely logical for the other timelines to be affected as well.
LMAO, love the meme.
Thank you, thank you 
Everything else regarding the world is open to interpretation.
When talking about the "unified time" at the end of Chrono Cross, I'm of the opinion that it's supposed to be up for interpretation and deliberately left vague. Schala calls to the player, not Serge, during her speech, so I believe Kato was trying to address us in his message; the ending is for us to decide.
But that doesn't necessarily unify the players who want a clear ending. So, we get great discussions like the one you're bringing up here instead!
If you look a little deeper at the poetic meaning behind it all however, the "scars of time" created by Lavos could signify a nightmare of the planet. The merging of realities and purge of Lavos/Time Devourer could also signify that nightmare coming to an end.
I like the metaphor you have for the "scars of time" being the split timelines. It makes sense. Those scars being the nightmares of the planet is also repeated very similarly by Robo in Chrono Trigger. He and the others suggest that the Gates are the memories of some dying entity (the planet) reliving its past.
So yeah, I could see the true purpose of the Chrono Cross item being to mend these scars. What that means, exactly, I'm not sure. It's difficulty for me to believe it's an actual merging of all timelines into one "ideal" timeline, specifically for the same concerns Lucca writes of in her letter: What of the other futures that are discarded? The other people? Some things may be fixed but many other things are traded for that to happen. Who's to say the Reptite dimension with no humans at all is not better and more "ideal" than the One? Who determines what gets merged?
To me, this isn't "everyone winning". Even in the ideal timeline, Lucca's fears of someone going back in time for revenge, effectively undoing it all, could still easily happen (unless time itself is somehow sealed?).
I agree that we should try to base theories on as much canon as possible. Yet, this is difficult when the games contradict themselves even. Trigger describes time travel with the Grandfather Paradox... yet promptly discards it for the rest of the game. Cross, unfortunately, has several contradicting elements: For one, Crono and Marle are both presumed dead (as seen by their "ghosts") and alive (as Lucca's letter, written sometime while Kid is still a child—thus after the fall of Guardia—speaks of "her friends" in the present tense); (2) When was the timeline split? In 1006 AG, when Schala reaches out to Serge who then comes into contact with the Frozen Flame? Or when Kid travels back in time to 1010 AG to save Serge? (I prefer this answer, myself); (3) Said time travel incident is itself a paradox; Kid goes back to save Serge... who will later go back to save Kid?
Oh, I also agree that there's a split in time before 65 Ma BG, causing the Reptite timeline to progress and later be involved in the Time Crash. I'm not set on the idea that it was Lavos who caused it, however. While Lavos definitely has some temporal powers, recall that it's the Entity who creates the Gates. Lavos may simply have acquired her time magic from the Entity in the same way she absorbs all other life. Before creating a pocket dimension in which to reside, Ayla says that Lavos literally burrowed deep within the earth. Otherwise, why crash into the planet at all if she could create a temporal pocket at any point and not kill off the creatures she needs to feed from? I think Lavos couldn't use time magic at all before consuming it from the planet, and even then, never in a capacity to travel travel or create Gates herself (though it could be argued that it was Lavos who sent Janus and the Gurus into the future, just as it could be argued that it was her who beckoned Chronopolis into the past—my theory's not perfect either).
Basically
1 - Anything that exists in Zurvan is not part of the ideal timeline.
2 - Only the real timelines of Home and Another unify because of "Angelus Errare" and no other.
I'm not quite a fan of the idea that there's a difference between "timeline splits" and "parallel universes". They seem kinda the same thing? Chrono Cross suggests and CT:DS outright confirms—through Magus right before the Dream Devourer fight—that "there are as many worlds as there are potentialities".
But let's supposed that there are "real timelines". I'd argued that's it's only Time Eggs or similarly very powerful temporal anomalies that create them. I put together this timeline to showcase that (and also to help myself in understanding the Chrono series' confusing timelines).
(apologies for small font, zoom in if necessary)
We have several of these "real" splits.
- In Pre-History, an unknown event causes a split. I believe this is caused by the Entity. In the timeline where Lavos never falls, we have the Lost Sanctum (Reptites, Dragonians, Dinopolis, etc.).
- In Keystone 1, we have everything that happens in Chrono Trigger up to Crono's death. If we go with the multiverse idea, every travel to past would also create another unique timeline.
- The Keystone 1 (orange) and Radical Dreamers (yellow) timelines are functionally on the same line; everything, including the party's many time travels, are the same, up to Marle's use of the Time Egg which causes the split and sets the resulting (yellow and blue) timelines in stone.
- In Radical Dreamers, Crono dies, permanently. The game Radical Dreamers takes place here, of course. Just... don't think too hard about moustache-Lynx and where he is elsewhere.
- In Keystone 2, Crono is saved by the Time Egg, and the party eventually defeats Lavos. Later, Belthasar and Robo develop Chronopolis, leading to the Time Crash.
- Time Crash happens, Another World is created. Eventually, Kid travels back to 1010 AG with a Time Egg to save Serge. Don't worry about the paradox.
- Home World is created. For some reason, Serge can jump across the pond to Another World. Here we have everything that happens in Chrono Cross, leading up to the Chrono Cross.
Everything after that is speculation and exactly why this thread was started! 
What's everyone else think of Sheiken's ideas?
- The merging of all the timelines would be the memories, souls, and realities of people all being weaved together in harmony. This means that no one in particular decides what stays, goes, gets altered, etc. It just happens in its most natural form. One would assume that it would try to resemble the unaltered timeline as closely as possible, but without Lavos and with influence from the different timelines that existed beforehand. And example of this is El Nido, which did not exist until after the Time Crash. However having it manifest naturally may not affect the base timeline in an unstable way, so it was written in. Also Kid being a reincarnation of Schala from the RD timeline rather than a daughter clone of Schala from Antiquity makes the most sense, and is also written in. The Dragonians would still exist as they not only existed in El Nido at one point in time, but they could have simply evolved with humans naturally without Lavos killing them off. Ayla even showed sympathy for Azala as Lavos was falling and Azala showed respect for Ayla in that same instance telling her to, "Take care of the planet." So it is not hard to believe that it is possible for them to find peace.
So in short, everything is simply weaved as naturally as they can be. Things that cannot be written in physically could exist in our minds through Legends and Folklore, much like the Chrono IP itself. You are right that not everyone would win. Lives that were once meant to be lived would change, and there is no getting around that fact. When I said that, I meant us as fans win due to the sheer potential of such a merge. But for those changed lives, it would not matter. Be they merged memories, folklore, or physical manifestation they will all be weaved together in perfect harmony as per the Chrono Cross. Time is not being fractured in this case, but healed in a way that would likely prevent anyone from messing with time again.
But if someone had to decide, it would have to be the Entity itself. In which case all of those dreams that were changed and weaved into a new existence would remain within Zurvan, as they have always been nothing more than dreams of the entity itself. No matter how you slice it, there is a dark side to the theory however. But for the cast and characters we see in both games, we have closure. That is the main point of a definitive ending theory afterall.
- Love the timesplit graph you presented, very good reference point. I do feel the need to correct one contradiction you said though about Crono and Marle however. The ghosts are only seen in Home World and Lucca's letter was written in Another World. Home world is also the timeline that tries to recreate what Crono and gang changed in the future, before FATE intervenes in the Dead Sea (which I assume was only possible because the Dead Sea itself was unstable). So I believe that when the split happens, they die and fail their quest in Home World. Perhaps by butterfly effect, but either more changed than just the point of Serge being saved onward, or they were simply written out of existence. Afterall Migeul does refer to them as "echos of a timeline that no longer exists."
Another possibility that supports them failing their quest is that under the assumption that they defeat Lavos in 1999 A.D., one of the changes that takes place in Home World is simply that they died in that battle. This means they would have never had the chance to return to 1000 A.D. to begin with, but Dalton would still be war hungry as he was defeated before the split. This could also be why the ghosts blame Serge for the future remaining unchanged in Home World, and how their work was "undone". This could also be why Kid is nowhere to be found in Home World, as she was only born into Another World as a daughter clone (remember, she was a reincarnation in RD timeline).
Another World however is said to be the reality we play in Chrono Trigger, and in this timeline they are alive and helped Lucca make an Orphanage for children who lost their parents in the Fall of Guardia. This is likely why there are so many pictures of them in Lucca's house, as if the kids met them. They are probably organizing a resistance or rebuilding Guardia while having conflict of Porre. Raidus refers to Guardia as "once peaceful" which could mean either destroyed or at war. The castle fell and Truce burned, we know that much but we do not know much beyond that. No matter the case, I believe Crono and Marle to be alive in Another World as there is nothing that suggests otherwise.
Thank you both for your input, very interesting stuff. Talking lore is always a good time, and we all learn from eachother in the process. I look forward to discussing this further.
