Plenty of shows need to hit their 2nd or 3rd seasons to really find their feet. Heck, Star Trek: TNG had a godawful Season 1. Seriously, go watch that stuff again. Horrible. Worse than any season of Star Trek: Enterprise, by far. I'm okay with a slow burn, as long as things accelerate, and that was happening in SGU.
The main difference really was that SG-1 and SG:Atlantis were monster-of-the-week episodic shows, and SGU was a season-long arc drama. I think a lot of fans of the former weren't expecting the slower build-up or the darker atmosphere, and that's what brought SGU down.