Being able to actually contact the people of Lavos would in a way be its own proof of humanity's worthiness as candidates for their "paradise of knowledge," much as the people of Vulcan weren't interested in Earth until Zefram Cochrane made his warp flight. Obviously, the people of Lavos stand countless light-years above the Vulcans, and almost any other race one could think of. They aren't like the Q, however. The Q are not nearly so powerful as the average person has been led to believe. For one thing, it's been fairly well proven that their power is the result of advanced technology rather than innate ability, and Q (the one played by John DeLancie, to avoid confusion) has been outwitted several times by the crew of both the Enterprise and the Voyager. And when you get outwitted by a crew like Voyager, that's saying something. I've sneezed boogers that could match wits with some of them; they ain't bright.
...did I mention that one episode where they miraculously escaped a black hole and thus broke nearly every law of physics that I know of and probably a bunch of them that I don't?
Anyway, Zurvan itself will have very limited "screen time" so as to maintain the mystery; only the final phase of the final boss battle would actually be fought there. Of course, Crono and Marle have to die in the ending, Robo has to become infused into FATE, and Schala has to be lost to the darkness of time. We already know the fate of Lucca; she has to return to her own time, and presumably Glenn would, as well. This leaves us but to decide Janus' fate, which will involve searching for Schala. I guess he'd end up staying with Belthasar. I think it'd be cool if he ended up helping Belthasar plan the events of Chrono Cross. I mean, no one brain could possibly put together all the minutiae of that plan, unless they're Lavos. It required an incredible knowledge of engineering, physics, mathematics, history, and just plain old balls. It'd also be rather fitting if he helped, both in terms of his personality and his destiny.
Any thoughts on superbosses? Maybe another one of Lavos' people? I'd rather not shoehorn in Omega Weapon, because that wouldn't make a lot of sense.
Finally, I think I've thought of a scheme that allows for Lavos' people to aid the team without acting as deus ex machinas, at least not in the conventional sense. It involves the final boss battle, which solves two problems at once, like so:
With the Frozen Flame in captivity in Chronopolis, the only pawn that Lavos has is King Zeal. As long as the Frozen Flame exists, his life force will continue to be sustained. Basically, they've got to kill him manually, or remove Lavos' hold on his mind in order to save the planet. King Zeal's objective in the past will be to destroy the nascent life force of Gaia, and in order to do this he'll need to get far enough down into the planet to actually access its soul. Within the context of Chrono, lifeforms that are not yet born are mere dreams in the sea of Zurvan. As the planet is "incubating," it's trapped in something of a dream state. Entering this dream state would be done in a similar fashion to using technology to hook someone's brain up and enter their dreams, but on a much larger scale. If one entered this dream, they would in effect be inside the planet's soul, and from there they could easily destroy it. However, he'll need the actual power to destroy it, as well as to get there in the first place; his labs have cooked up a crazy soul-eating bioweapon based on Lavos himself for that purpose. Lavos can absorb souls, as demonstrated by both his presence after he landed on Earth and his union with Schala in Chrono Cross. But, as Lavos isn't around to work his evil magic, King Zeal's labs have coughed up a bioweapon suitable for the task. The resemblance shows; it's going to be the ugliest, vilest creature any of us can think of, both physically and morally.
To this end, I suppose the first part of the final dungeon might resemble Final Fantasy VII in its form, because they're going inside the planet, but its latter parts would be progressively odder because of the nature of their mission, which requires the team to enter the planet's soul as well. Once they reach the periphery of Gaia, I propose a "seal" mechanism that King Zeal would implement to keep the team out. This would not be unlike Ganon's Tower in Ocarina of Time, where Link had to release six seals, one for each elemental power, in order to disable the shield blocking the way to Ganondorf's throne room. In this case, the seals would not be for each element, but would instead be representative of a different Chrono setting. This would accommodate the Calasperan setup. Once the final seal is broken, the gateway to the altar of Lavos would be open, where King Zeal would be activating the bioweapon and preparing to sacrifice the soul of the entire planet to the Beast. The problem, of course, would be actually getting to the seals, which is where Lavos' people could come in. None of Belthasar's technology has the power to do this, and neither does any other technology of the year 2302. It can only access the spirit plane in a very roundabout way; that of traveling through time. Lavos' people would naturally be sympathetic to the plight of the Earthlings; their goal was to get worlds to grow and thrive, and Lavos is interfering in this process by having his minions effectively destroy the planet before it's even born; basically, he's violating the Prime Directive. However, they wouldn't simply do the job for the heroes, either; that would be just as much of an interference...that and they don't know whether they're strong enough to beat him in all his hatred. The deciding factor lies in the heroes themselves. Their personal fortitude has been proven beyond even the possibility of doubt, having actually faced Lavos' physical form and defeated it, banishing him to the Tesseract. But why did they bother, the people of Lavos ask? The destruction of the world was well outside of their lifetimes, and didn't affect their lives at all. There exist two reasons that they decided to help; first, they believe that what Lavos is doing is fundamentally wrong. But second, and perhaps even more important, is that they believed that the planet, their legacy as human beings, was worth fighting for. But the world of 2300 A.D. had given up on itself, content to let Lavos kill off humanity. The people of Zeal, the greatest sons of Earth, had grown decadent and lazy, and it destroyed them. The Middle Ages had fallen victim to petty bickering and racism, and in Crono's time, imperialism is in the process of destroying peace. Gaia's successful attack on Lavos had not relied upon the rule describing its lifeforms, but the exception. Humanity was an exception from the very beginning; they weren't even Gaia's desire. It was only because of Lavos that they were allowed to survive, and even now it would seem as though it's trying to kill humanity off, judging from the Time Crash (which will be addressed as part of the El Nido scenario).
Thus, humanity's ultimate test, that of survival and the assertion of destiny, comes in two parts. For part one, Lavos' people would modify the Epoch's engine to be able to generate a temporal field allowing the team access to Gaia's inner core; this would be the limit of their aid. The team would still have to defeat King Zeal and his crazy bioweapon by themselves. The second part is for humanity to forever rid themselves of the scourge of Lavos, as he's still alive, and operating from the Tesseract, where, after the final battle, he's consuming Schala's powers to evolve into a Time Devourer. Basically, Chrono Cross stands as the fulfillment of humanity's test, not only to the people of Lavos, but to ourselves and our posterity as well; they've achieved the virtue of knowledge. Once that has happened, the path opens to harmony of the spirit. The ultimate destiny of humanity is of course left untold, because (surprise) it hasn't been written yet. That's our job to find out.
For the actual mechanics of the final battle, King Zeal would first take his normal form. Phase II would consist of a battle with the bioweapon, after which Lavos makes a key mistake; thinking that nothing can now stop his ascension as the supreme ruler of Earth, he releases King Zeal from existence to focus all his weapon's energy on assimilating the world. The bioweapon, however, accidentally assimilates King Zeal before he can disappear from existence, a condition both allowed and magnified by the chaos of souls and time that the weapon is creating. Once this occurs, a rather lengthy cutscene about King Zeal and his relationship with Schala, Janus, Queen Zeal, and the world at large commences. After that, the final fight begins; the bioweapon's evolved into a much stronger form, resembling the Lavos shell (only much, much uglier and covered in satanic imagery) and the background for the fight is a distorted version of the time bubble from the first game. However, despite its increased strength, its soul is now contesting that of King Zeal for dominance, and this weakness is what the heroes exploit to destroy it. Even moreso, King Zeal informs the heroes that they can weaken it by using the Chrono Break. It still has a bit of Sorin's life energy attached to it; allowing the weapon to assimilate the Chrono Break, and thus Sorin, who bears nothing but hatred for Lavos, results in the weapon's very existence starting to unravel, and it needs to absorb the power of Zurvan to survive, rendering it even bloody uglier than before and causing it to change forms and weaknesses periodically. After a harrowing final battle, the weapon has been weakened so much that it's taking in too much of Zurvan's power to focus on assimilation, but this will destroy the entire universe if left unchecked. Thus, it needs someone to strike the final blow. However, once this is done, the sacrifice will stop, and whoever isn't out of the dreamworld will vanish into Zurvan along with the bioweapon and King Zeal. The same chaos observed inside the ruins of the Black Omen begins to take shape, only this time, it's much like Daniel described the gateway between worlds, with each portal leading to a different timeline altogether; in effect, it's much like the people of Lavos describe the first ages of the universe. Schala is ensnared by a portal that emanates from the bioweapon, and Janus is outraged. Crono naturally volunteers to strike the final blow against the machine, and Janus objects all the way, screaming that he has to get his sister back. Crono eventually just knocks him the fuck out and orders Lucca and the remaining party members to GTFO, because if they don't they're all fuckin' dead. Marle stays behind with him, because she knows she can't live without him. The others escape in an Epoch that ends up trashed after the fact; by the grace of Lavos' people, they're afforded a time portal back to 2302, where Chronopolis has manifested in reality once again. From there, the ending commences.