Well, I don't pay close enough attention to get all nitty-gritty with gameplay mechanics, but w/e...
Flo-mo: there's a lot that could be improved here, but I'll try to be brief. Most worlds were incredibly spacious to accommodate for this mechanic, but when you got stuck in a smaller space, it hurt bad. Case in point: the old parts of Traverse Town. I don't even want to think about just how many times I dodgerolled into a wall, got stuck in place while flo-mo activated, and promptly got murdered by some Dream Eater.
I'd say dodgerolling should not activate flo-mo, or the player ought to be able to deactivate the mechanic altogether.
Fighting: It's no secret that everything, from the bosses to the lowliest mook, got shot up with steroids to compensate for the player's many advantages. I can deal with that. I'm also not too bothered by the brokenness of Balloonga, because when it comes down to it, it's the player's choice whether to abuse it or not. What annoys me is when simple Keyblade melee damage is next to negligible. Make Keyblade attacks relevant again!
Time travel. Well, along with A LOT of other weird stuff that happens in TWTNW, just explain it a bit more clearly. Perhaps include a detailed and explicit explanation in the glossary? I just know that it took me years to understand some of the stuff that happened there.
"Oh, that was part of my master plan all along, lol." Yeaaaah, this definitely needs to get re-worked. I personally believe that Xehanort was bluffing about planning for every. Single. Thing that has happened so far. But if I could get in there and actually change things, I'd have Xehanort indicate that while his plans hit some rough patches (all of TAV's accomplishments, basically), he was able to shift gears and readjust his plans. Being a "devious tactician" doesn't always mean you have to pull off a flawless Xanatos Gambit; creativity and ingenious flexibility are some of the traits that I admire the most in a villain.
Really, I find the ability to redirect a failure into an eventual victory is much more interesting than setting up a convoluted fixed game. Seriously, where's the fun in a game you can't lose?
Sora. Just... tone down the dorkiness. I think he acted less childish when he was young and naive back in KH1.
Some would also want Mickey to tell Sora about the danger of the pain that's lurking in his heart, but I don't really see how it would make a difference at all. The guy will try to help anyone who's hurting, even with full knowledge that he'd be putting himself in mortal danger.