I think part of the reason why I like Stargate Atlantis fic and fandom more than the SG1 fic and fandom I've seen is because they have a larger and more developed ensemble cast outside of the main team who are around all the time, which lends itself well to long, broad stories encompassing the entire city.
For instance, off the top of my head for SGA I can list: Lorne, Zelenka, Beckett, Elizabeth, Miko, Chuck, Parrish, Grodin, Kavanagh, Woolsey (if you count season 5), Ford (if you count season 1), Stephanie Heightmeyer, Katie Brown, Halling, Caldwell, Jeannie and her family, Bates, Cadman, Keller (again, if you count later seasons) Michael the Wraith, Todd the Wraith, etc. etc!
For SG1, there's General Hammond, General Landry (if you count S9-10), Doc Frasier, Walter, Siler, um, that geeky scientist guy I can't remember his name who's around sometimes with the glasses, Bra'tac (sometimes), Major Davies (sometimes), Jacob Carter, Maybourne (sometimes), very occasionally Sha're and Skaara, and lots of people who just kind of skip in and out of the series once in a blue moon.
The whole close, cohesive, large, and diverse Atlantis community just appeals to me more storymaking-wise, I guess, or at least that's part of it. There are so many more interesting personalities to bounce around! And that automatic closeness, sense of community that we get an impression of from them being pretty isolated in Pegasus is not something we ever really feel from the Cheyenne SGC base in SG1. As a whole, I mean, of course there's teamyness galore in SG1, and I include Hammond and Frasier in that. But it's not the same.