Season 1 of Atlantis was its best by far; it went downhill in varying degrees from there.
It was very effective at establishing setting and characters, and using those to tell an overarching story within the confines of an episodic, adventure-at-a-time format. Later seasons tried the same kind of pattern but didn't pull it off nearly as well.
Later on, the show seemed to suffer from the belief that rotating out cast members was the best way to keep things feeling 'fresh,' but all that did was fall into the same old formulas with new faces. It's a fun watch, if you're looking for something frothy and fun, but much of SG-1 does that better.