I see your point, but if 'The Trust' exists then it would have designs on Atlantis. They should have seen this coming, and really it means that Earth is completely infested. I liked the fact that Atlantis was seen as still in contact with Earth and what's currently happening there, while seeming very remote.
I didn't like the 'reset button'. I would have preferred that Caldwell/Goa'uld was killed or escaped. Even though it kind of explains Caldwell's recent behaviour (how long has he been a Goa'uld) I actually didn't think it would be him.
I think there is a loss of direction in Atlantis. They had the big battle with the Wraith at the end of Season 1, in much the same way that SG-1 had the big battle with Apophis. Now they have nowhere to go with the plot that makes the same impact. Having the Wraith fight each other makes them a weaker enemy without making them more interesting. The Wraith can't get to the Milky Way without getting to Atlantis, or getting an upgraded Asgard Hyperdrive, and that wouldn't be an option if TPTB want to keep the two shows separate (though why then introduce the Trust to Atlantis.)
I agree with you that something new and extra-ordinary needs to happen if this franchise is to continue. Unfortunately, we will probably have to wait until the Season end cliffhanger for it.