Atlantis couldn't decide what it was, I think. They got to some great characters, but with difficulty. Ronon replaced Ford in Season 2, with Ford being a very poorly written character, he didn't get a single interesting scene for a season. Weir was remarkably poorly written IMO, every time she made a decision it was wrong. Teyla had great moments but in too many episodes she was a "mystic Amazonian alien" cliche. Early on Atlantis tried to again do the "small band of humans versus powerful alien enemy" thing, abandoned that, transitioned to a cornier version of SG-1, then also abandoned that and went more for character stories, it was a mess. I'm also simply not a fan of its too lighthearted style, it intentionally avoided the more serious bits of SG-1.

Universe was great in my book. Detractors say it's like Stargate trying to be Battlestar Galactica, but BSG is easily my favorite sci-fi show so I actually liked that. Universe did make some mistakes early on, but the second season was great, I enjoyed Dr Rush as a very non-Stargate style main character, and I enjoyed how Universe had a completely different take on aliens, keeping them mysterious.