Most liked:
Axel, just because i hated him at first, and then towards towards the end of CoM, i started to see that there was more to him then the firey, jerk face he drew himself out to be. Then In KH2 i saw he had a softer side, and Days really made him my favorite. Just how emotional he was, and the inner struggle he was faced with. It really did prove there was more to him than the spiky hair and smart-ass remarks.
Xemnas: I usually hate villains, but something about him was different than other villains. I think it was his lack of emotion (duh), like he didn't get up us soras face or do anything extremely evil like XH did in KH, I just didn't get the instant "oh this guy is giving me bad vibes". He was relatively calm throughout it all.
Roxas: I liked him from the beginning, though he did somewhat annoy me at times. But he is just so angry throughout KH2 and the end of days; I admire that. Angry protagonists are the best.
There are other members such as Xigbar, Siax, and Lexeus that I don't know what to feel towards currently, but i know there is much more to them and I will hopefully touch base with that info when BbS comes out.
Then the ones I didn't care about: Deymx, Larxene, Zexion, Luxord (almost forgot all about him actually.) and Marluxia.
I hate Vexen. I hated him from the start and I hate him still. Then Xaldin, he gave me the villain vibes, and I honestly think he was the most evil in the organization.