I just realized that I'm not highly involved in some of the fandoms of the shows that I watch. Therefore, these opinions may or may not be unpopular! I'll be guessing on some of them.
1. Steven Moffat is vastly overrated. He's good at creating very intense and scary situations, but they fail to hold up under any sort of logic, including story logic. He has no concept of actual character continuity, not just with other writers in the series but with his own writing as well, however, he never forgets to make nods to his own previous cheap gags. This shows very clearly where his priorities are and, as far as I'm concerned, his association with DW should have ended with "Curse of the Fatal Death". That said, as long as he doesn't write it as set immediately following the previous episode, I probably will enjoy his S4 two-parter the first time through and I think I'll just avoid watching it a second time, so that the shine won't come off (the only episode of his that I didn't enjoy on first viewing was GitF and even that one was visually gorgeous).
2. Martha Jones was criminally underwritten for the most part and was used more as a plot device than a real person. And though Freema has a lovely smile and seems to be a wonderful and interesting person, she wasn't a strong enough actor to carry the character through the patches of thin writing. However, when the writing is good and playing to Freema's strengths, she's more than up to the task ('bones of the hand' is just a great moment, period).
3. The reason that Donna's cool is because she understood and connected with the Doctor on a human level, not because she smacked him around.
1. Hmm. What's unpopular in this fandom? With regards to Obi-Wan -- Qui-Gon/Obi-Wan squicks me because it reads far too much like a father/son relationship. This is also why I didn't start shipping Obi-Wan and Anakin until the third movie -- Anakin reacted against Obi-Wan in Clones in a very 'rebellious son' sort of way. They were firmly equals in RotS (particularly from Obi-Wan's perspective) and that actually finally made the Republic Trilogy slashy for me. Before RotS, I was very gen (TPM) and het (AotC) focused in the fandom!
2. Speaking of non-slash, I really like Padmé. My favorite Obi-Wan/Anakin stories are ones that deal realistically with the fact that Anakin loves Padmé very deeply but also that his love for her and the manner he chooses to express it are destructive elements in his life.
1. Much as Ruby and Bela kick ass (and I do enjoy both of them greatly), I wish that we had a reoccurring female character this season that wasn't evil or dead. I'm vastly disappointed that Ellen vanished off the radar and that we didn't see Jo again after she finally got interesting (but, of course, if she's no longer a love interest, then she doesn't count. /sarcasm). SPN has been disappointing me a lot with its writing of female character recently and with Dean's attitude towards women.
2. Cassie ("Route 666") was a strong, vibrant character who meshed really well with Dean. I felt like her character's choices within the episode always made sense and I understood both why she slept with Dean and why she said good-bye to him at the end. Cassie = fabulous.
3. I don't get the squee over the matching Winchester tattoos. Not my thing.