I guess I'm the only person who thought that establishing contact with Earth sooner than expected was a good idea. If they didn't then it would have been another Voyager-esque unlimited supplies situation. At least with regular contact with Earth, it was one less thing the writers had to worry about (let's face it, only nuBSG has been able to write good stories about limited resources). Plus, it kept both 'gate shows tied together (something none of the modern Trek shows had been able to do that didn't have the foul stench of a ratings stunt).
As for things that should have been, like most people, I would have like to have seen Jackson more. I mean, He's a linguist with an interest in the Ancients and he was among them for a while. It would have been natural for him to be more of a presence there, if not take over once Wier was gone.
Also, they could have pulled back on the Wraith after their initial introduction and make them this unknowable background threat, thereby making them more ominous and scary. I thought that this would have been the chance for the SG:A writers to show the Trek writers how the Borg should have been done. As for a good, knowable advaersary, they could have focused on the Genii as the main villan. They were just humans that were very agressive and overly paranoid with the facade of an agrarian society. In some cases, they were scarier than the Wraith because, under the right circumstances, the Atlantis expedition could have been the Genii.
Also, they could have found a way to bring Robert Patrick's character of Colonel Sumner back for episode or two. They were able to bring back Kowalski in SG1. Why not Sumner?