I don't really dislike a lot of characters (and sure as hell hate none of them) at the moment, but there's quite a few I actually used to dislike.
Remilia - I thought she was a stupid brat in IN, but that's kind of her shtick and I don't mind her at all now
Eirin - her incredible arrogance in IN made me dislike her initially, but now she's alright
Koishi - I hated her concept and thought she was incredibly creepy, but then I realised that I love depressing characters with concepts I hate and she jumped up to my favourites. Interestingly enough the only character I liked before I encountered her in a game.
Yuuka - never knew why she was so popular and the fandom sadist interpretation just turned me off, but she's yet another character I've grown to tolerate
Yukari - I actually liked her quite a bit until I read SSiB,
However, thanks to Rise of the Evening Star, I've gone to appreciate her a bit more again.
Yorihime - take a good guess. I still don't like her, but she's interesting and has a neat design.
This is more of a meta-dislike, but I seriously don't understand how this fandom likes Momiji and friends so much more than actually interesting characters like Kanako and Eirin. I mean, I'd really like it if ZUN gave Momiji some more screentime (and dialogue!), but until then, I feel she has no right to be liked that much.
I mean, even in polls, I'm inclined to rank my "disliked but interesting" characters higher than random stage 1 bosses I don't care about.
oh, there's also Kikuri who is fucking creepy and I don't like her