I'm not sure that announcing the cancellation so early in the season was a good idea. The production was already too far along to make any major changes to the material as a whole, and it's left me with a distinct "lame duck" impression of the season arc. Whatever they throw at me, I have no confidence that it will find resolution before the end. It's inevitable that the first couple "Atlantis" movies, just like the "SG-1" DVD films before them, will be devoted to wrapping up loose ends.
It's not that this episode was lacking in the thrills of discovery and adventure; it was one of the best episodes of the season thus far. The guest appearance by Daniel Jackson made perfect sense under the circumstances, and the interplay between Jackson and McKay was genius. And the writers certainly developed a credible threat, upending some of the ongoing plot threads in some unexpected ways.
I liked the new enemy, even if I had been hoping that the aliens from "The Daedalus Variations" would have made another appearance. I'm going to go out on a limb and assume that this new threat is actually an old threat in new clothing, so to speak, based on Daniel's realization at the end of this episode. At the very least, it could serve to bring some of the disparate elements of the Pegasus Galaxy together if they were an evolution of a known quantity.
It was interesting to note that a weapon that hadn't been used for millennia was so familiar to Todd. Was it something so catastrophic to the Wraith that they passed down stories about it? He even knew it by name! Granted, it was necessary for Todd to recognize the weapon and its probable source for the plot to work, but it seemed a bit too convenient.
Far better was the conversation between Todd and Dr. Keller regarding the gene therapy and its effect on the Wraith. Todd is very candid about his intentions for the experiment, but more so regarding his misgivings. I thought his point was rather well made. After thousands of years of culture built around the culling of humans, it's no simple thing to alter their feeding habits. This touches back on elements of "The Queen"; Team Atlantis is so focused on what's good for them and humanity that they utterly overlook the perspective of the Wraith.
I found that far more compelling than the usual mid-season finale fireworks, and it's too bad that the focus is always on the action instead of character. Todd's turn against the humans had nothing to do with philosophy, despite all the foreshadowing. Leaving out the new enemy and the supposed death of Radek and Sheppard (which will never happen) might have been less explosive, but imagine a scenario where Todd's decision to take control of the Daedalus was based on his inevitable conclusion that the Wraith would never change and that the alliance was hopeless. Played right, it could have been far more effective, and it's a shade less than perfect as a result.
In the end, despite the Jackson/McKay show and the exciting chaos of the final act, I couldn't shake the feeling that the show was still suffering from its "lame duck" status. I keep looking for more, because I know each episode leaves us with less.