In the end, I think the thing that makes an AU work or not work is characterization. Of course, that's my key point for all stories, and with Atlantis I find myself accepting a narrower range of option than I have in other fandoms.

Hmmm, interesting--I find I can enjoy a wider range of situations, and even characterizations, with the Atlantis crew in an AU than I've been able to with other fandoms/pairings. There's something about John and Rodney that translates well all over the place, for me. As long as some essential (to me) characteristics remain, I'm pretty open to enjoying all types of AU with them in it in a "Whee, this is fun!" way, more so than I would be with, say, Jim and Blair, Xander and Spike or Mulder and Krycek. I feel the need to keep John and Rodney tied very closely to their canon selves less, though, as I said, their essential qualities, those things that I appreciate most about them, need to be present, at least in part. But, the closer the AU gets to canon, the more I want to see them portrayed as they are in the show, and, for non-AU stories, I really want that characterization to be spot-on. Hmmm, again.