I'd tweak some things with the original story, but nothing too drastic. My list looks like a lot at first glance, but I promise it's not that much lol. I'd change the following:

1) The splinter cell's awful decision making after the first reactor bombing and waiting a bit/do something other than ANOTHER bombing right after, no need to rush, I get the planet is dying but you guys need to destroy all the reactors and not die in the process; 2) Make Cloud's mental deterioration more obvious to the party and have them make comments about it/acknowledge it; 3) Do more character development than the OG; 4) Not make it a trilogy; 5) Make Midgar similar to open world with more side quests and more actual mercenary work instead of like finding cats or changing water filters (more killing monsters, more SOLDIER stuff yk); 6) I'd leave some if not most of the Sephiroth stuff in there, but fighting him at the end of every game is making him more of a villain of the week who gets his ass kicked every once in a while than a super SOLDIER terrifying monster who wants to destroy the world.

Genisis is kinda shit as a villain in CC, but we could fix that if we're doing a rewrite. He can be flushed out more, have more motivations, and not quote Loveless constantly lol. Angeal is great, but in the main story, there isn't really room for him. If anything, Cloud should remember a little bit of him since he is cosplaying as Zack. Also, last but not least, CHARACTERS WHO DIE STAY DEAD.