Seeing as the series has finished: SPOILERS ABOUND (for all SG series)!
How strange for this thread to be bumped today! I started watching Stargate at the beginning of April, and went through all of SG-1, Atlantis, and Universe, finishing just last night.
As much as I loved SG-1 and Atlantis, towards the end they were just so samey. Atlantis was SG-1 in another galaxy, and you could have taken any one character out of either show and put them in the other, and nothing would have changed. Sure, the team dynamics in the first few series of SG-1 were really good, but it grated on me that new actors and faces simply assumed, for all intents and purposes, the same character as their predecessor. The only character I can think of who was totally different is Vala, and she didn't really appear at a great time...
SGU, on the other hand, was completely different, and I think that's why I enjoyed it so much (out of the three series, I'd say that SGU is my favourite). I will say, though, that that not having a real "enemy", despite the rather fun, non-English speaking, recurring alien species, meant that SGU lacked some structure, and it became particularly evident when Rush turned from being the shady scientist with a hidden agenda, to being a reluctant team player.