You mean besides the obvious?
I'd have to say...the seagull whose egg was stolen.
Seriously though, for me it'd be Huey, Louie, and Duey. I know time flows differently in all worlds, but how on earth are they still kids in 1 if they're the same age in BBS? It's like a mistake against nature. It bothered me too much, like that nagging feeling on the back of my head.
Secondly, ACT, because those three are a ticking time bomb, especially now that Remake is out. I shudder to think how Nomura is going to keep certain kinds of fans satisfied (because we all know they're there, no matter how much we deny it).
I'm not sure what to feel about Yozora though. Yeah, we know he's practically Nomura's saltiness made manifest, but the silver lining in this is since he's a KH character, Disney owns him, so Square can't really screw Nomura over this time, at least, not without the looming threat of a lawsuit or majority acquisition looming on their doorstep.