I think some of you forget that by and large all Kingdom Hearts villains are pretty one dimensional. That's really to be expected in a game that dichotomizes good and evil based on fairy tales.
Xehanort's Heartless? Think his hammy ass is well developed?
My point being, whether it's one villain or thirteen, it's pretty obvious most of them weren't supposed to be developed. So it's not even a matter of "thirteen is too many so they won't have enough time to develop." That is, the scope of the villains does not affect their depth- you're not trading one for the other. Hell, in a game explicitly devoted to them, we really didn't get any character development, save for the obvious (Roxas and Axel) and one or two not so obvious (Xigbar and Saix- though I'd hardly call it "development").
And don't give me this garbage about how the CoM members were better developed. Screen time doesn't equate to development. The CoM members, from beginning to end, were just as stereotypically one dimensional as the other members, and even more so in some respects. If you want to argue that individual KH2 Organization members didn't get enough limelight or exposition, fine. But personally, I enjoy when a villain is shrouded in mystery, when their motives are unclear. The KH2 Organization was more of a dark horse simply because we didn't get constant cutscenes between floors (or in this case, worlds) explaining what they were up to.
Now, as for my thoughts on the biggest plot-wise issue, I was really not a fan of the second visit formula. Each visit felt like an isolated "episode," but I'd have rather had one long visit instead because, more often than not, the second visits felt even more like filler (except, maybe, Agrabah). Also, while pretty much most of the games suffer from this, I really disliked how they rushed everything at the end. Killing four Organization members back to back? Yeah...
I would have much preferred for, at least, say Xigbar and definitely Luxord to have been killed at Land of Dragons and Port Royal.