Ooh I like this thread.
The entire Honey Bee Inn section of the game simply wouldnt work well in 2015. The mini quest of getting Cloud to be the chosen girl is fun and adds some quirk to the game, but that entire section is just something else. Keep the cross-dressing stuff but add different things in the place of HBI.
Yuffie and Vincent cannot be optional. They should really add things into the game where you cannot miss them. Make it so you recruit Yuffie in Junon and Vincent in the Shinra Mansion.
We should know Rufus Shinra survives. Him showing up in Advent Children doesnt really make sense when you see how his tower was obliterated with him in it. Make it so the Turks get him out before it happens.
Expand upon the Chocobo racing stuff. Give us leaderboards and let us actually enter leagues in the game. Make it into its own fully fledged DLC expansion if you have to, because it has the potential to be fantastic. Same goes for the bike and snowboarding minigames 
