I think what really ruined the show was all the character shuffling. I thought the show was amazing at first; it had a really fresh feel to it, being in a long-lost city of a somewhat mysterious alien race instead of just a military base. I liked all the main characters a lot, personally.
But they had to mess up their little family, getting rid of Weir and Beckett was a bad idea, and bringing on Sam and Woolsey (much as I love Robert Picardo) was just bad. The Replicators were annoying, I thought we got rid of them in the last show? They just seem like those ants that invade your house every summer that you just can't kill completely. Bringing back Beckett was good, but trying to sort of bring back Weir was weird.
They shouldn't have made a ton of changes to this show. It was fine the way it was.
Just wanted to throw my two cents in. I'm so sad they ruined a good show like that >.<