Damn you Hadji!
I wanna see the final battle! Anyway, that choose the character thing was a cool idea (that was in Suikoden III too I think. I've only got the manga seeing as the game was never released here) and the backstory for Sephiroth was a cool idea, and the war thing was nicely done. How'd he survive 240 years though? Minor complaint is that Kefka's sprite could have been recoloured to represent an original character, but hell, he didn't appear for that long anyway.
The Crono and Dante fighting the monsters parts were well done, and again the music was put to good use (glad you aren't just relying on FF/CT music, the Skies of Arcadia music is a nice touch).
You go into my fave authors, and this submission goes in my faves too. I eagerly await part 5. Hope it comes out soon.