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, where she is intentionally made out to look like the bad guy in the first half and never really recovered for me. I wasn't even sure whether to support Yukari or Toyohime in the forest scene because I just couldn't stand her (Yukari, that is). I really disliked how everything went her way all along and the fake anger near the end topped it off.
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