I've found that the Alien Base missions tend to boil down to a slog in the first room (usually resolved with lots of C-4). This problem is only made worse by the fact that the alien defenders will see and shoot my soldiers through solid walls (sometimes two sets of doors). I'm not sure if the Wraiths are supposed to exhibit this behavior, but they all teleport directly into the starting room on the first few turns. I actually like the idea of being pinned down, but I expect the aliens to be held to the same rules as my soldiers, and when they don't it tears me out of the experience.
I'd like to point out I've been playing since some of the earliest builds (posting for the first time) and I think the game has only gotten better, but the better it is the more these kinds of things seem to stick out.