There were a lot of couples I think should have got together and never did.
Obviously Janeway and Chakotay should have got together, they had great chemistry, but it seemed a determination of the writers to keep Janeway single.
Also Seven and Harry Kim. Kim's pining after Seven throughout Season 4 meant he shared a lot more scenes with her then Chakotay, in fact, you could argue that he was being built up as a potential love interest, and it makes a lot more sense when you consider the only reason Kim was kept on post-season 3 was because of the actor scoring high in a Top 50 men, or something.
I would have liked Julian and Jadzia to get together, but I'm still happy they remained as friends.
Jake and Ezri is another couple I think should have got together. Although I liked Ezri ending up with Bashir, it would have been even better had she gone with Jake, the scene they shared in Shadows and Symbols showed a lot of chemistry, and, and this is always my reasoning, it would have earned Jake the status of main character for Season 7.
As for Picard and Crusher, I was annoyed when the movies didnt show any of this, although I did like that they got back together post- Nemesis.