The Ark of Truth was a pretty good movie, but the stuff with the Replicators was certainly a low point. Replicators are just worn out, and "enough is enough." That said, the Terminator Replicator was kind of cool.
Unfortunately, we never really do get any kind of decent resolution with the Ori invasion. Yes, the Ori themselves are gone, and the Priors no longer believe, thereby stripping Adria of her powers. But the Priors still command starships that are practically undefeatable, an army equally as powerful and have a foothold in the Milky Way. Do they really just pack it up and go home.
On the nitpick side of things, early on in the movie, in the briefing discussing a plan to destroy the Supergate, Mitchell asks why they just don't try another plan of connecting it to a gate near a black hole in Pegasus. Carter says they coan't do that due to the risk of being attacked by the Wraith. If that's the only thing wrong with that plan, why not just do it with a black hole in the Asgard's galaxy?