Season 1 is the best part of the show, but you can tell that in their zeal to avoid a middling first season like SG-1's, they rush things a bit and don't take their time to explore the city as much as they should. They honestly could've made The Eye S1's finale and pushed The Siege to S2 by making up the gap with city, planet of the week, and Genii episodes.
I think where it starts to lose its luster is in S3, when they make the Asurans (aka Replicators Redux) the main baddies and then contrive reasons for the humans to not use anti-Replicator guns on their planet, because they couldn't think of plausible reasons for Earth not to wind up curbstomping the Wraith (such as personnel shortages keeping them from fully exploiting an entire planet
covered in Ancient tech). Michael was also a bit of dud villain, although Todd and the Genii (pre-coup) were pretty good and could've been long term villains if there had been a bit more thought put into their stories.