The Goa'uld were some of the greatest characters on the show, and I think Atlantis really suffered from not having villains that were as rich, compelling, and just plain screwed up. It's kind of like Batman ridding the world of the Joker, Peguin, Bain, and Riddler, and then just devoting himself to fighting a pernicious and invasive species of crabgrass that's taking over Gotham's lawns. No matter how fancy his Bat Sprayer is or what perils he faces, weeds just can't carry a scene.