I liked Universe a bit more by the end of the final season, but it had a lot going against it
1) They tried a bit too hard with the "grimdark" or Moore's BSG style of drama. It just didn't seem to fit with the IP, though
2) Them constantly being on the move meant there was never really a good villain/foil, or even recurring allies
3) Too many unlikable or bland characters
4) They went too hard on their attempt to reduce "power creep". By the end of Atlantis, Earth is basically a super power in the galaxy. The whole "cut off" I presume was their attempt to "nerf" Stargate Command, but it also felt too isolated from the rest of the IP as a result. Granted, I know Atlantis had a similar period, but they shifted away from that fairly quickly