xD I liked all the options, but I'd rather stick to my own opinion. *ahem* Chrono Cross is a good game, but if I managed to hack it then I'd change, well, everything!
For one, I'd change the setting of the story. Being good at storyboard plotting, I'll manage to do that with sufficient amount of time, linking it properly to Chrono Trigger/Radical Dreamers with great respect. Although, I wouldn't intend to "revive" some of the dead characters (well, I could revive Magus). I wouldn't really remove the characters already playable in-game, except for a few useless ones, and group them accordingly; say a group of playable characters that are involved with the story greatly and have good personally developments, and another group of playable characters who aren't useful for the story and are just there for fun's sake, except for minor side-quests/stories (I'll give that to all characters) and certain secrets. So the major characters would only be a few.
Next, I'll keep the current stamina battle system with innate, but somehow shorten the LOOOOOOOOOOOOOONG battle transitions. Well, an active battle would be great too. xD I'd also give Guile a priority, and at a certain point revealing his true identity as (duh!) Magus, where all his old spells and stuff is unlocked. The character will then change his appearance from Guile to CT style Magus. He will be the one to rescue Schalla. And pretty much, I'd say that the so called "Time Devourer" really sucked! =_= Lavos seemed more intimidating than it. SO I'd change EVERYTHING about it, giving it a far more scarier appearance and battle formations than Lavos, including it's spells and skills. FATE also sucked, and I'd do the same with it.
Another thing that would make CT fans cling onto Cross hack. xD Secret playable characters that have some connection with the old CT. Give the characters more background story, and making them interact with other playable characters to give more depth. Give more skills and spells. Enable exploration outside El Nido, including exploring Guardia and Medina, etc. Implement Time Travel. Make Glenn learn about Frog (LOL). The true mystery of Ayla and Leah. Ayla's baby (W00T). Several alternatives resulting in several different timeline effects. Secret bosses and items.
Okay, I think I mentioned too much. But I must say I have a LOT more ideas where THAT little thing came from. XD So you can see, I wanna do everything in my power to (BE A GOD AND) change the game and make it several times interesting driving the gameplay to it's apex. Plus, I hated the way it connected with Chrono Trigger, so yeah.
P.S.: Did I mention I WOULDN'T let Prometheus (Robo) die either?! And someone *secret* appears and fixes him?