The initial promos for this episode made it look rather generic. Given how this season has progressed, that wouldn't necessarily be a surprise. The writers have finally turned an eye towards character arcs for most of the cast, something that had been lacking in the past. Unfortunately, it has apparently been at the apparent expense to the potential season arc.
This episode might be the beginning of a change in that perception. That would be fitting, since the episode itself defies the impression given by the promos. Instead of a character-heavy tale, this is all about the future of Team Atlantis as a whole and the fate of the Pegasus Galaxy.
In essence, a man with visions (explained rather well within the continuity of the Stargate universe) guides Carter and the rest of the team through a crisis involving the Wraith. Specifically, it involves the Wraith from the third season episode "Common Ground". His relationship with Sheppard makes this a lot more interesting, especially given the stakes.
In a certain sense, the decision to reprogram the Replicators to pursue and destroy the Wraith made sense. It would protect Atlantis, for one, and that would continue to aid humanity's interests. On a practical level, it pulled back the galactic threats long enough to give the character arcs a chance to develop. It also happens to give the revelation in this episode additional weight. While Team Atlantis has been dealing with personal issues, the Asurans have decided on horrific new tactics.
Objectively speaking, the Replicators use a logical tactic. If you want to eliminate an enemy and care nothing about conserving common resources, elimination of the food supply would be effective. Unfortunately, in this case, the Wraith use humans as food supply, so the end effect of the reprogramming has been a major negative. Team Atlantis ultimately feels responsible (and rightfully so), and it doesn't help that rectifying the situation means working with the Wraith, who have fragmented even further in the wake of the renewed Replicator attacks.
This adds a sudden sense of urgency to just about everything, which the writers will hopefully recognize. This should add to Carter's impression that the job is too much for her (an unexpectedly good character turn), and there are some interesting connections to Teyla's quest to find her people. McKay should find his brilliance challenged, and Sheppard will need to deal with his relationship with his Wraith "friend". It looks like the promised blend of plot and character arcs has finally arrived!