I haven't watched too much of Stargate Atlantis, but I liked what I saw. I've seen all 10 seasons of SG-1 atleast twice, so I plan on watching atlantis eventually. As for Universe, I've seen 3-4 episodes, and I really disliked it, so I don't ever see myself watching any more of it.
I recently started streaming Netflix and hadn't seen any of the Stargate series (did see the original movie.) I watched the first several episodes of each series and for some reason, Atlantis appealed to me the most. I finished watching it and then moved on to SG Universe, mainly because there were only 2 seasons and I figured I could finish it quickly and then tackle SG1's 10 seasons.
I'm over halfway through SG Universe's second season and while I didn't like it that much at first, it has grown on me since I stopped trying to compare it to Atlantis. It's definitely darker with less humor but the stories have been interesting. I'll be sad to see it end so quickly.
I'm sure I'll feel the same way when I finish with SG1. I hope to see another Stargate series someday, I'm really enjoying them.