Off the top of my head: They re-established contact with Earth too quickly.
There was a off-world, colony feel to the show early on which I really enjoyed. Cut-off. Limited supplies. Limited friends because they were new to Pegasus and didn't know anyone.
I think the writers could have played that out for a bit longer.
Then there would've just been comparisons that they turned the show into the Stargate version of Voyager, IMO.
You mean what's happening now with SGU?