First one: What if Chronopolis is destroyed? It would make a reason to return to the End of Time, and give another reason to why the Chronopolis in Chrono Cross is different to the one in CE(and doesn't have the TDC).
This might be difficult because we need to avoid permanent settlements in the End of Time, because Belthasar wants to hide knowledge of the Fall of Guardia from the party and Gaspar. If they would stay at the EoT long enough, they might learn about this event by observing the timeline. The Chronopolis location will probably be augmented a bit though, perhaps with some room for Gaspar, etc. It already looks like a very subtle, early version of the CC time fortress actually, with the elevator that leads to the underground Powerstation with Mother "FATE" Brain guarding it.
Second: Currently, we have the entire crew from the orginal game, why don't we replace Ayla with a reptile from the other dimension? He/she could have conflicts with Chrono stopping King Zeal from causing the Atash Kedah, but in the end decides that he/she shouldn't be the product of a time traveller's actions (his creation is the cause of King Zeal stopping Lavos) but when Zeal is stopped, he/she still lives because of TTI. This further fuels his/her rage for King Zeal and remains with the party until the end of the game, at which point lives out the rest of his/her life in the reptile sanctuary you wrote about in another topic.
God damn it I hate it when I write so much for something that will never be used.
Personally, I think this could be interesting, but... we might alienate fans of Ayla by doing this (or not?). In any case, I'd rather wait until human Glenn is real before considering another PC replacement.
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About the Frozen Flame:
I think it could be very effective to show it and reveal its name for the first time at Lavos's Crater. The details about its uses can be explained normally in Belthasar's files, but perhaps it could be referred to only with cryptic names or periphrases like "a strange Red Rock", etc. The players would be curious; some might guess that it's the Frozen Flame, or not... In any case, they'd be amazed in the climactic Atash Kedah scene to see a weird "ammonite" sprite opening itself to reveal the famous CC Frozen Flame. Then King Zeal would finally refer to it as the "Frozen Flame", and the name would stuck.
Perhaps he should also reveal at this point that the Flame's creation was accidental and that the destruction of Zeal was caused by Lavos' attempt at claiming it back.
The KRS: Are we dumping it? I never thought it was very necessary.