I like the majority of the things already mentioned here, but the one thing I really like and extremely impressed with is the overall presentation.
The developers at Square went above the call of duty with the menus and layouts. The unique command menus are a delight to watch. I sometimes stop just to look at the menus and notice the details. Not only that, the menus that appear when you accept a mission in one of the worlds (like in Land of Dragons and the Underworld) are amazing. Each one of them are designed according to the theme and characters of that world. Square could've just made a generic menu and that's it. But then went to add small details that while you may notice them but actually adds to the overall experience.
Even the generic menus used in the main menu and save menu shine, with small details like changing character artwork whenever you save. Again, simply amazing.
The graphics are also awesome. You can tell they spent more time designing the characters. I mean, in the original KH Halloween Town Sora used the stiff face textures during cutscenes. Now Sora is very expressive even with that costume.
I could go on and on about this. I am extremely impressed with how the entire game is presented.
-pap64