I actually liked SG-U and the direction they took, I thought that their big problem wasn't so much as the darker tone as much as it was rather slow and boring up until the second half of the season. They took a little too long to get into the meat of the story for the season and just bored the audience with lots of darkness, and to make matters worse, they didn't seem to learn their lesson from S1 and did the same thing in S2, start off really slow and pick up around ep. 11. I think that if they had continued with the action and used the momentum of the last few episodes of S1 for the first episodes of S2 they might have kept enough viewers around for SyFy to give them a S3, but instead they kept the same slow, plodding pace and drove all but the most die-hard fans.
There's also the whole gimmick of being cut off from Earth, you knew that that wasn't going to last very long, show runners just have no faith with that premise and always have to try find a way to get them back in touch with Earth before long. They did that on Voyager, it happened on Atlantis so you knew that it was going to happen on SG-U as well, although it was a little surprising that it took as little time as it did from them to reconnect with Earth. I wouldn't be surprised if they planned on completely re-establishing contact with Earth sometime around S3 and having them traveling back and forth via the onboard Stargate on a fairly regular basis, just like they did on Atlantis.
