Atlantis is cool, bad guys are actually threatening, the cast is fun, and the world building doesn't go of the rails as much as SG1 in the later seasons. It strikes a good balance between serious stakes and more light hearted space shenanigans.

Universe is... different. It's a very serious show, that clearly tried to have a tone similar to the Battlestar Galactica reboot. Sometimes it works, but it's hard to see where it was going (literally) before being cancelled.