I want them to add dungeons into where you go and get, KotR, HP<>MP, Quadra MAgic, instead of just hey you made it here take an item, I think they would be decent places to add content IF they are actually planning to truly add any content. Maybe just a post game dungeon where you get to fight Genesis or something along those lines if they absolutely feel they need to tie the games more heavily together, or even something that is related to Advent Children. That being said, I agree I would not like the main game changed to accomadate the other iterations of ffVII but as additional content after the end of the game rather than shoe-horned in.
Bookmarks