SGU's main problem was that it took too long to go nowhere. Other problems included that lack of humour and light-heartedness which are trademark to Stargate and attempts to take themselves too seriously resulting at the best of times being boring, like their depiction of aliens. Or at the worst of times they look totally ridiculous doing things the other Stargates could get away with, like depicting the Lucian Alliance as a bunch of cliche cartoon supervillains.
Yes, SGU did show some improvement with the second half of the second season, primarily they were starting to figure out which characters worked and were given them more to do. But it was too little, too late. The damage was done. While SGU might not be the worse show on television, it's a far way's from the top indeed.