I liked what developed between Sisko and Kassidy Yates. I felt that as relationships went in Trek, it was not only believable, but mature and enjoyable to watch.
I didn't like any of the relationships on TNG. They were either dreadfully boring or just plain weird. No chemistry, ever.
I hated Miles O'Brien's relationship with Keiko. She was whiny, rude and constantly disrespectful. Before somebody jumps me about saying "a woman should respect her man", that is not what I mean by that at all. I mean that in a good marriage, there is mutual respect. Keiko talked to Miles as though he were a five year old, and for a reason I can't fathom, he just took it. She knew she was marrying a Starfleet engineer when she got into that relationship. Harping and nagging on him about her career needs not getting met was just stupid, considering she
made that decision.
I hated the Worf Jadzia pairing. No chemistry at all. Then again, I don't like Worf, so I don't think any pairing for him would've worked for me.
I wish they had let Andrew Robinson have his way about portraying Garak as bisexual. The friendship chemistry he had with Bashir was more interesting than any
romantic pairing on that show. I wouldn't have even cared if Bashir didn't feel the same way because he was straight. Just allowing that issue to be aired would've been nice. Most portrayals of bisexuals I've seen in tv and film are either horribly campy and over the top, like the MU characters, or make them come across as manipulative psychopaths like in Basic Instinct. As someone who is bisexual and has known it pretty much all of my life, I find such characterizations insulting. I think Robinson would've handled it in a mature, interesting way, and I would've loved to see it.
EDIT: I think the reason I find the characterizations insulting is because so often film and tv writers use bisexuality as shorthand for "perverted" or "twisted", much like some authors will turn a character into a rapist for no other reason than to show that character is evil. It's lazy, and it's unnecessary. There are other ways to establish that without maligning an entire sexual orientation.