I'm reading the plot, so far it's been pretty good not too much to gripe about but there are some issues regarding the effects of time.
Now I know that it's a bit wonky in CT how time travel affects the party, but here's an example of something I'm not sure of.
The team demands to know what happened, and how his predictions on the outcome of the Porre event could be in error; Belthasar explains that the timeline has been not only changed, but fundamentally altered by a catastrophic error, but he is unable to pinpoint its source, since the changes are subtle;
So what had just happened prior is that Belth said "Don't worry it'll be fine nothing bad will happen" then the 3 go back and the bad thing happened. After they return to the future Belth says, "Oh that's wierd that shouldn't have happened."
Again it depends on how we treat the time travel but this leads to some issues. I haven't played CC so I know nothing of FATE or Chronopolis directly but we can't assume all players to have played CC in the first palce so the concerns need to be addressed I think.
If you go back in time and things get altered, when you go to the future, those altered events are now the ONLY past that exists. So when the 3 go back to Belth after seeing things go wrong, Belth would say, "What do you mean? Of course stuff went bad, that's what happened, I have to reason to say otherwise"
Nor would he be able to track timeline changes due to subtlty. If the changes are too small to be able to pinpoint that means Belth is using a fact checker to determine changes. You'd in theory have an "old" database for comparison to a "new" changed database. However this can't exist because as the timeline changes so would the "old" change. This is a bit rambly and hard to follow so.
How will timetravel actually affect things? Because if we have 3 different styles of time travel effects it's going to be wierd (the reason I dislike that Marle disappeared and then reappeared because her ancestor returned, it doesn't fit the same mold as much the rest of the affects.)
Yeah, that's basically what Belthasar says to them. You're pretty new to the site, so you might not have read all of the various theories on time travel that have been established. Like any model or set of models, there are limitations to their utility, but they're the best we've got right now to explain the various phenomena seen in the series. There are two concepts from CT that lend to this formula of a timeline that dynamically changes; they're loosely based on real-life situations in relativistic physics.
Concept number one is Time Error. It basically states that if you go back 400 years into the past and stay there for five minutes, when you return to your era, five minutes will have passed in the present. Gates propel you a set "distance" forward or backward in time, not to a certain point. If they only took you to a certain point, they wouldn't be visible or usable at any other time coordinate, anyway. Corollary to this effect, temporal changes are not visible to observers until a point in Time Error at which they're actually put into effect. Without King Zeal's interference in the Porre/Guardia situation, it would have panned out more peacefully, but he doesn't actually put his plan into effect until between the team's arrival in 2302 and their return.
Concept number two is Time Traveler's Immunity, which is a bit bizarre and irregular. Basically, once you've traveled in time, you're immune to changes in the new timeline; you've already created another timeline just by being there, and you have no origin in this new timeline. Therefore, nothing done within that timeline will erase you, and it's impossible to access lower-order timelines or Time Errors except under special circumstances. Equivalent forms of you get Time Bastarded and sent to the DBT; this isn't like being killed, it's merely being subsumed into a more "senior" form of yourself from a lower-order timeline. The only way to actually eliminate someone with Time Traveler's Immunity is either to kill them manually, or to go back to the timeline in which the lowest-order form of them originated and destroy them there before they acquired their immunity. Normally, this isn't possible. However, the Chrono Break is explicitly designed to do this.
The Marle paradox was abnormal, as it was effectively a grandfather paradox, a feature that the series doesn't focus heavily on; it's best to say that Crono and Lucca were unaffected by the results, but Marle was, or that they ended up in one of two possible timelines that resulted from the paradox. Either way, outside interference is required to resolve this, and that's what Crono and Lucca provide.
As for Belthasar, he possesses Time Traveler's Immunity from being sent to 2300 A.D., so he can observe the changes in the timeline. He performs similar activities in Chrono Cross.