I've long held the first season of Atlantis in rather high regard. In many respects, it's nearly perfect (in terms of the pacing, characters, setup, writing, and story arc).

Unfortunately, they also kind of wrote themselves into the perfect dead-end scenario. They'd stacked the odds so high, and put it to the climactic test, but didn't have a solid strategy for how to continue the conflict and story arc without pulling an obvious rabbit out of the hat.

To put it into context, once the Wraith started actually gunning for Atlantis, there wasn't a clear path to prolong that conflict in a convincing and non-repetitive way. The setup already made it clear that they were almost totally unopposed and unchallenged in the Pegasus galaxy, and didn't have a great deal of internal conflicts (Not at the start anyway). And it's not like they had no idea where Atlantis was. They had the means to get there, the numbers, etc.

The writers chose to dodge and delay the whole conundrum by simply... cloaking the city after nuking the atmosphere to make the Wraith think they'd blown up the city.and making everyone think it was destroyed. Clever in some ways I'll admit, but ultimately it feels like a bait and switch in terms of plot flow.