Get rid of the love subplot. It legitimately added nothing outside of making Squall randomly decide he wants to save princess plot device in Disc 3. If you have to have the subplot, give them some actual chemistry please. Thats a hard sell in an FF game though.
Make everyone but Squall a lot less fucking stupid/insufferable (Excluding Lagunas silly ass, and Krios/Wards cool asses)
Remove the completely unfounded GF memory erasure shit period, thats stupid as fuck no matter how you look at it. It also makes Irvine look even dumber than he already is for not saying anything for two discs. And doesnt explain why Seifer never forgot either. Just make it so they were all in different Gardens, they meet, oh we know each other haha we have this in common, okay were professionals now lets move on.
Ultimecia was stupid. Just make Adel more important than what she was since she already fit the bill of known psychopathic sorceress and was clearly shown to have reach far beyond what she should have been able to what with the freaky radio messages and body snatching.