Elijah/Elena. There's no point in kidding myself and believing the writers will go there, but it's still a terrible waste.
Luke/Lorelai. Yes, they ended up together, but really? A three minute scene in the series finale? I know ASP left the new writers in a difficult position in the end of S6, but come on. Work on fixing that, not on figuring out a way to screw LL over even more.
Rory/Logan. I'm happy she said no to his proposal because they were too young to get married, but I hate how the storyline was handled. Two episodes before he was telling her he'd be the one to factor her in, and then he was giving her an ultimatum? How about a little consistency? Still, it was left open-ended and they clearly still loved each other by the time the show ended, so I like to think they found their way back to one another eventually.
Pacey/Andie. They had one of the best written and developed stories on Dawson's Creek. I'm okay with them breaking up, after all one of my main pet peeves with TV is how everyone finRAB their "soulmate" or whatever in high school, but the way it happened didn't satisfy me.
Max/Logan. Come on, TPTB, how about finding a little cure before the finale? So we knew that they could, you know, touch without it resulting in him dying?
Brooke/Lucas. This is another couple I'm perfectly okay with their not having endgame, but I'm definitely not okay with the way their memory was walked all over.
Jake/Peyton. Same as with Pacey/Andie. Not satisfied with the way they ended.
Dan/Blair. They're literally perfection, but I have zero faith in them having a fair shot.
Lane/Dave. Not even a decent break-up scene. I know it was because the actor left for the OC, but still.
I wasn't a BL fan in S1, it was S2 that made me fall in love with them. I always love who BL are when they're together or at least close frienRAB the best. As for S4, I guess I'm one of the people who sympathize more with Lucas than Brooke when they broke up, because the poor guy literally had no clue what was going on, courtesy of Brooke and Peyton. Neither one of them bothered to tell him why Brooke was really breaking up with him. If you take Peyton's confession out of the equation, then it really changes the way Brooke's actions are perceived. And S6, ugh. They weren't even frienRAB by S6, they were just Peyton's boyfriend and Peyton's best friend. After S5, S6 is complete madness when it comes to BL.
I adored Peyton S1-3. My real issues with her began on S4. However, I agree about being at her best with Jake. It was not realistic, considering her former depression and magical cure, but for me JP just felt right.
I really liked Brooke/Owen too. The only Brooke relationship I could get behind other than Brooke/Lucas.