Well...my only concern about that would be that Lavos doesn't want that Zeal to remain in the sky, since he presumably destroyed it for getting too powerful. We can dodge that bullet with the new one, possibly...thoughts needed.
Here is my idea to wrap up the remaining plots:
Dalton / King Zeal
Belthasar still wants to make the Chrono Break, and Gaspar doesn't quite know this yet as he's been conferring with Melchior. Belthasar notes that throughout Zeal were some refined magical conduits, sort of acting as transmission lines and buffers to power the islands. These would allow high magic energy input to a construct creating the Chrono Break. Getting them from Zeal would be impossible without severely disrupting history, as they'd literlaly have to dismantle parts of Enhasa, Kajar, and Zeal Palace. But there's another option: they can probably find some in 11998 B.C., especially if Dalton stockpiled some. The party hit the ground running in ancient times, learning of Dalton's hideout at the icy lake. Upon reaching him, Dalton boasts that he's soon going to have the power he desires -- that all this equipment he's gathered will soon grant him the "staying power" he desires and enable him to get revenge on his enemies. He reveals that his plans begin in a few hours. He laughs that it is convenient for Crono to show up, since he can start his revenge early by killing the party. The usual tsuff in the plot outline happens and Magus kills him. They enter his storehouse and acquire the conduits and return to Chronopolis. Before the screen fades, King Zeal arrives and laments that Dalton is dead, but smirks that he can "participate in that little revolution" himself now.
What I'm going for here is that King Zeal visited Dalton and promised to take him to Crono's era to wreak havoc. This wouldn't change time at all -- originally, Dalton never did regain any power or influence, and in the new timeline, he merely participates in the Fall of Guardia with the Porre army and later dies. Since Dalton dies, King Zeal decides to show up at the Fall of Guardia himself. Of course, if this all happened BEFORE the party went to 11998 B.C., then Dalton would still appear at the Fall of Guardia, which could make things interesting. But of course, we could have the party come to 11998 B.C. before King Zeal ever gets there to complete things for Dalton (in history from a Time Error perspective, if that makes sense). If we use this, should we have Dalton and King Zeal both, or just the King?
Anyway, after they get back, Gaspar takes the conduits and destroys them. Belthasar explains that...due to recent discoveries, they won't need the Chrono Break. The party can go to Chronopolis's lower levels and talk to Melchior and Gaspar to learn more. Melchior will hint that Gaspar absolutely blew up and forbade Belthasar, while Gaspar will talk about the extreme danger of the Chrono Break and how using it to kill one person is purely excessive.
Proto 5-02C
Since the Chronopolis outrage is squashed, then yeah, there's not much to do here. But with him, it'd be easy to have the party bump into him right after acquiring the repair part from Johnny. Proto could notice their unique fashion and generally greet them in a friendly manner, making for some small talk. The party could then sort of talk about how the old Proto has been lost to the changes in time...just like the old Johnny. It'd be sort of a reflective sad moment.
Comments?