I like that Atlantis had a bit of shiny but also a bit of tarnish to it. The characters are not flawless and, when faced with particular issues, do not always make the best decisions, sometimes leading to morally questionable outcomes. That the writers of the show are willing to do this in order to create an interesting story and source for discussion is something I admire. The result is a much more human and down to earth story. As such, I've never really watched anything from the SG franchises for the sex appeal, though some of the actors are hot.
Also - Ben Browder always struck me as being a little smarmy. Whether this is carry-over from his character on Farscape or just the way he acts all the time, i don't know. But given his character's more or less the shiny hero, it's sort of a turn-off for me, to be honest 