Stargate: Atlantis has always lived in an uneasy place between interesting takes on well-executed standard Sci-Fi plots, and completely generic takes on standard Sci-Fi plots (including the tendency to leave the world of our heroes essentially unchanged, at best leaving a seed for a later better episode to draw on). One gets the feeling that the way that things work in the writer's room is that the powerhouses say, "OK, we need to have A, B, and C set up in episodes before our stuff airs for sweeps or finales."
So far this season is the latter - nothing changes except a plot element that can be summarized in a sentence ("Ronon is hooked on Wraith enzymes and turns on the team, but he's okay now... for the moment"): I'm hoping that they're saving their A-list episodes - they tend to be written by veterans of Stargate: SG-1, who are at least add some ironic recognition to the times they use boilerplate SF plotting (eg, when Jack snarks, "didn't I see this on Star Trek?").
So it goes. I have to wonder how many of the people who keep rating this stuff highly have seen much of past SF series (including a few times in SG-1), since this kind of plot has been seen so many times before it ought to be issued a standard serial number, just like the joke about prison inmates memorizing the joke book ("Some people just can't tell a joke").