I do think there's something to the idea of Spock as a minority. He would have faced the prejudice that a minority would face in our world, while Uhura wouldn't have faced racism on 23rd century Earth. For what it's worth, both actors are minorities as Quinto is gay. I think it's possible that Quinto uses that in his acting, as Spock as a sometimes abused outsider has been really well done.
I think people can not like Spock and Uhura as a couple without it being racist. They may want Uhura with Kirk instead for example. I am slowly liking Spock and Uhura more, a strong story for them in the third movie with better writing could make me a bigger fan of them. They were better in the first movie.
I kind of agree about Troi and Tom Riker. I ship Troi and Riker hard, but I did get frustrated at how he kept her on the backburner until he was ready for her (and it worked!). When Tom Riker came along I was really rooting for him to get Troi since Will had been playing her for so long. Of course, that didn't work out, and in the end I was very very happy for Riker and Troi to get married.
I also really like Picard and Beverly, they should've gotten together sooner, and I hate that the movies didn't get them together but at least the books did.
Speaking of books, I love Calhoun and Shelby from New Frontier. Their romance is beliveable and well written, touching and sometimes strange.
I did like Spock and Zarabeth - love Yesterday's Son - but Spock's best match was the Romulan Commander.
Kirk and Edith were pretty cool together, but you know he'd have left her if he could get the Enterprise instead. No woman can keep Kirk.
I always wanted Jadzia and Bashir, and Worf and Ezri, so of course the show paired them up the other way. I thought Worf really brought Jadzia down, she always was having to jump thru hoops for him and his Kingon bs, while Ezri didn't put up with Worf's crap. I feel like Jadzia had a bit of a romanticized view of Worf while Ezri could see the real Worf more clearly, so their relationship, even if not romantic, was more honest.
I always rooted for Janeway and Chakotay, if only her command situation didn't make it impossible. *sigh*
Tom and B'lanna were a good couple, they had a lot of angst to work thru, and the writers actually took time to develop them as a couple over the years.
Sarek and Amanda did have a great relationship, I just wish she'd have set him straight over how he treated Spock so badly.
So, in short, my favorite tv couple is Riker and Troi, my favorite couple from the lit is Calhoun and Shelby.