I have two big things. First, I think they needed to be cut off a lot longer, and have there be a much bigger focus on them being cut off. I think an interesting plot would have been if they actually either lost Atlantis at some point or had it destroyed, so they were on the run, or had to try and retake it from an old enemy.
My second thing was the replicators. Now, I want to say that I love the Replicators. The bugs are awesome, and SG1's human-forms were a good concept. Atlantis' replicators aren't straight up bad, but it annoyed me because it seemed lazy. We are in a new series in an entirely new part of the universe, and we still have Replicators. Wraith: Good, original idea. Genii: Good, fairly original idea with lots of potential. Replicators: Retread-ville.