Azarath, I think I might have some ideas over what to do. I think those sentences shouldn't be part of the beginning of the game, but rather, kept in the middle somewhere. Have the beginning start off slow, sorta having the drama build up towards the war between Porre and the El Nido Archipelago. I think instead of the hero being Crono, it should be his son if he did, indeed marry Marle, and according to your ideas, the game seems to take place after Crono Cross. Give this new character (referring to Crono's son) a name, believe it or not, I think Sandy would do him justice, it might sound majorly wussy, but trust me, I did my research, it's Greek in origin, and means "One who tries to save the world daily". And yes, it's also a guy's name as well as a woman's. Look no further than the baseball player Sandy Alomar, Jr. 'Nuff said.
Crono should appear within the plotline, and definitely, the idea of him having the convo with Magus is a brilliant idea, and could be used as a key turning point within the game when things are starting to get really ugly. Have the descendants from the other characters, like Serge and Kidd, appear within the game. And a new villain isn't a bad idea either. I'd have to say the idea of there being Lavos Spawns makes sense, but I think there should be someone behind the scenes TRYING to manipulate the spawns to reproduce, kinda like how Queen Zeal was trying to summon Lavos artificially.
Anyway, this is just the tip of the iceburg of some ideas. Do you have AIM Azarath? I think you have an awesome idea, it just needs a bit of work, and I am certain if two minds did work together, it could all come together brilliantly. PM me, I encourage you to do so.