I totally agree with what you and The Wormhole said. Atlantis in its first two seasons was pretty damn good, and although it stumbled through the third and fourth seasons, it was starting to pick up in the fifth season. It was a much more balanced show than SGU, where we did get some darkness, but it never became overbearing and there was a bit more humor to lighten things up. I do think that the writing staff was tapped out once they hit S3, since most of them worked on SG-1, so they really should've gotten lots of new writers who could add their own take to the show.
In all honesty, SGU appears to be a ripoff of Atlantis in several ways and given the lack of Atlantis references in SGU, I think the producers wanted SGU to be Atlantis done "right" and cover up what they perceive to be an embarrassment. However, SGU is an utter failure creatively and it came out too late to cash in on the "dark" show trend of the first part of the decade. It's the wrong show at the wrong time; people want something lighter to allow them to escape the problems we're having right now with the economy and everything else, not make them more depressed.