I think one of the major problem as mentioned before somewhere was the lack of 'plausible world building' going on with SGA, it continued over again from SG1. The problem that they've always had, is they add one thing in without adding a value or realizing the effects of such an encounter on the political, strategic and galactic scape of things. It was simply, add this in because it was cool, oh wait they are now over powered, better nerf them to buggery. The episodes First Contact and Lost Tribe is a prime example, adding in a kick ass new race that then suddenly gets the holy retard brick to the head then they lose all that ability in the space of ten minutes, or next episode.
They were supposed to be at war. I wanted to see the Atlantis crew building alliances with the hidden technological races (that were oh so many yet we didn't see any of them), stop with the whole 'only we can save you' stuff which grew sickening. Also, when you have a war, actually make it a war, a long drawn out bloody conflict that will last for some time. The end of SGA could of been, ok we've defeated the Wraith, but they will still be around for generations to come. A
lso No more bloody god dam magical plot devices that solve the problem in the last 2 minutes, you have a problem? Couldn't solve it? So what, deal with the consequences of failure, work through the adversity. And naturally give the rest of the damned team something to do, the annoying fact that it was always Rodney who solved things grew beyond tiresome (which is why I liked the episode Trinity because he failed in that, showed the reasoning of Shepard also).
Babylon 5 and DS9 showed great examples of how to win a war while at great cost to the individual and group as a whole, I kind of wanted to see more of that within SGA, little more pragmatism. My opinion I know