I'm sad that I'm so late to this discussion, but I agree with every single one of your unpopular opinions. I should probably pop over to the S7 thread at some point, because I have lots of thoughts about why I like it so much. Basically, I see it as the only season to engage with the idea that there might be a life for Mulder and Scully outside of the X-Files, and I like that. Mulder and Scully kiss and the world doesn't end, Mulder finally accepts his sister's death and allows himself to stop looking for her, and there's a general sense that both Mulder and Scully are slowly turning away from the X-Files and toward each other. I adore the scene in Requiem where Mulder tells Scully that the costs are too high and there has to be an end. In a way (another unpopular opinion, maybe) I wish the X-Files had just ended there. It would have been such a realistic, human, adult way to end the show, to have Mulder and Scully decide to cut their losses and live a life together while they still have the chance.
Related unpopular opinion: I like Sein und Zeit/ Closure, largely because of Duchovny's acting, which I think turns a nonsensical storyline into something transcendent. Which brings me to unpopular opinion #3:
Although I find Duchovny to be a more uneven actor than Anderson, I also think that Duchovny at his best is better than Anderson at her best. This may be just because Mulder gets better writing and more consistent characterization than Scully does. But when I think of the moments in the X-Files that I find particularly moving, it's often because of the subtleties of Duchovny's performance. In the bed scene in "Plus One," for instance, I think both actors do a great job with pretty terrible writing, but the moment that really sticks in my mind is the way Mulder's voice goes flat on "That's what you mean."
Opinion #4: I know I'm not alone in this, because someone upthread mentioned it, but I find Mulder much more interesting than Scully. (Again, I think that's because the writing for Mulder is generally better. It's Mulder's obsessions that drive the narrative forward, and I think the writers have a hard time figuring out what to do with Scully when she's not reacting to Mulder.) I will watch Mulder-centric episodes till the cows come home (I even enjoy 3, because I'm a sucker for grief-stricken, self-destructive Mulder), but I find most Scully-centric episodes to be merely depressing without really being interesting.