I think the biggest change I would make to the X storyline is have a greater emphasis on the Keyblade War. To me, while I otherwise enjoyed the entire X story, the biggest missed potential was that it didn't really focus on the actual war, aside from the ending of Browser X, which was only the final battle, and the X-Blade isn't even mentioned. What I would have done instead is have the first season end on The Bell ringing to signify the war, and have that be a cliffhanger. Then season 2 would have focused on the Player fighting in the War.
In Xehanort's reports in BBS, he mentioned that the war was a massive conflict, where worlds that did not go into battle eventually found the war brought to them. He also mentions that the fighters in the war were defenders of light, servants of darkness, those who wanted to reconcile the two, and those who were motivated by nothing more than lust for power. For the Season 2 plotline, the Player would travel to Disney and Original worlds that have been affected by the war, with the Heartless as well as Dark Keyblade wielders being the main enemies. Along the way, Player would meet wielders from all of the aforementioned factions. They would befriend fellow light wielders, with the Dark wielders being the main antagonistic force. Player would also meet wielders trying to balance light and dark, akin to Riku, which would serve as a lesson to Player that dark does not necessarily mean evil. Then, a secondary antagonistic side would be those driven by power. There would be several events where the Player would face off against this faction, to which they would also attack the Dark wielders as well. They would be the type that would attack any faction so long as it meant getting what they want.
This is really the only thing I can think of that really should have been explored.
