I was particularly fond of Atlantis season 1 because of its tone. The expedition was completely cut off from Earth in a galaxy where they didn't really understand the rules yet, facing the nigh unstoppable wraith. The season felt like it had a well-defined arc from arriving in Atlantis and awakening the wraith, leading to the inevitable attack at the end. Taken as a whole, it's probably my favorite single season of the franchise.
For me, the problem with Atlantis post season 1 was that the show never really felt like it knew where it was going to me. The constant cast changes and the introduction of newer antagonists felt like desperation to me. That's not to say that I thought the average quality of the episodes went down over time, but rather that the show felt somewhat less than the sum of its parts. Despite the huge body count racked up by the end, the team felt no closer to achieving their goals than they had at the start of season two. Standalone episodes had a feel to me of "we've already seen this".