Now, it's entirely possible that these episodes will have many moments in them that I end up liking. In this run of rewatches, I've often been pleasantly surprised by episodes that I remember being disappointed in first time round, probably because my fallible memory had forgotten all the fun bits, and dismissed the entire episode as "bad." I do, though, have particular issues with the whole Michael storyline, which I won't go into here (mostly because until I've rewatched the episodes, I can't speak with any real knowledge, only distant, hazy memories.)
However, thinking about it, I realise that I do not, in general, like season finales or mid-season two parters. This doesn't just apply to SGA, but applies to most shows that I've watched. Since the main point of these episodes is to do something huge and wonderful, that will haul in viewers, I am clearly out of synch with most of the audience here.
In many shows, I feel an almost audible changing of the gears for the two-parters, that can, in my opinion, jar with the rest of the show. I used to be a huge X-Files fan, and I did actually enjoy several of their two parters (mostly, I have to admit, because Mulder had a habit of getting injured in them) but I usually felt that they fitted in badly with the rest of the show. The two-parters were all full of doom and gloom, with huge storylines happening, and the main characters suffering awful things, but by the second episode of the series, the bad guys had backed off, and Mulder and Scully were back to investigating lizard men and killer rabbits, with no sign that the awful experiences had affected them at all.
Im general, I prefer smaller scale episodes that focus on the core cast, and allow them the space to shine. In SGA, the two-parters often brought in the entire extended cast, and I sometimes felt that the plot was too crowded for the core characters to get their proper time in the sun.
I'm also not a fan of long action scenes, especially ones in space ships or cars, when the camera focuses on things, not people. Car chases bore me. (They also make me boring and responsible and grown-up, and start tutting in horror at the awful risk to all the other innocents on the road.) Space battles bore me, especially when it's just distant views of big ships hitting each other. I lose track of which ship is which, and I just want to fast forward to the end, so I can see who's still there. (I do, however, rather like action scenes when the participants are wearing historical costume and waving swords around. Yup, I'm shallow that way.)
Additionally, when it comes to rewatching, I generally prefer episodes with a lot of humour in. Serious, emotionally draining movies might wow me the first time I watch them, but the ones I rewatch will be the black comedies and the satires (and, yes, the ones in which the participants are wearing historical costume and waving swords around.) I've rewatched certain humorous Buffy episodes a dozen times, but the big, portentious angst-ridden ones I've probably never rewatched at all. When I stumble on a series of Buffy repeats on the UK Sci-fi channel, I tend to skip the season finale type episodes, and only watch the self-contained monster of the week ones.
But I am clearly out of synch with most viewers here. I see on Gateworld that some of the highest rated SGA episodes are those with a cast of thousands and loads of space battles - episodes that wouldn't feature in my top 50, let alone top 10. But am I out of synch with the average fanfic writing/reading sort of viewer? I don't know. I've often noticed that the episode preferences of fanfic circles are rather different from the episode preferences of other corners of fandom. I'd be interested to know.