Think the big two are Rory and Sookie. Sookie was a very funny and sweet supporting character for a long time, but I think post-marriage she did become more annoying and unlikeable in general. I like her and Jackson as a couple, but I do think that marriage brought out the worse in her at least.
Its a classic opinion on Rory. But the 1-4 Rory was thoughtful, smart and fun to be around, later season Rory just became too smug and let her lifestyle go to her head too much. She still has her moments, but I much prefer her in the first 4 seasons.
The other ones are to smaller degrees. Logan grew on me, after not liking him at first. There are still many things I don't like about him. But I am at least convinced that he has more depth than first appears and probably does care for Rory.
It was reverse with Dean. I never loved his character but thought he was decent to be around and quite liked him and Rory as a couple for at least a season and an half. The longer he's on the show the more self-important, bland, and whining he became.
Jess I like and now see as Rory's ideal partner (at least out of her three main love interests). But he was a bit of a slow burning character. When you understand more about his background and see how he matures later then I think I understand him more. And always enjoy the spark he brought to the show.