If there's one seldom-spoken truth about Team Atlantis, it's that they repeatedly underestimate their enemies. They operate with the questionable confidence of those who have survived on a combination of luck and determination. Success often breeds contempt, after all. But when one looks back on the series as a whole, the victories have been surrounded by vast fields of defeat.
Whether it's the Genii, or the Asurans, or the Wraith, Team Atlantis has been more than willing to ignore the intelligence of their enemy, even after they've been fooled in the past! Todd has been a worthy strange bedfellow since he first arrived on the scene, and he has been quite good at turning situations to his own advantage.
Granted, the usual suspects were wary, and they knew something wasn't quite right. But this is in part due to a very Western trait: dismissing the importance of understanding the enemy's culture and perspective. Quite frankly, Team Atlantis has a rather poor track record when it comes to intelligence gathering. They rely on convenient allies for key information, and this has come back to haunt them on more than one occasion. (Similar to how often the worst situations are a product of their own mistakes.)
It might sound like this is a complaint; it's not. If anything, it has been the mantra of the Stargate franchise from the beginning. The reason why the IOA is so potent a force in the Stargate universe is the simple truth behind their oppositional stance. The Stargate program has initiated a number of problems since its inception. On the other hand, they've also been the solution to those problems, and the end result has generally been positive.
The allure is watching the team get out of each and every new mess. Too often, in the past, this was left to Sheppard and McKay. In a nice twist, their best intentions are actually more dangerous than helpful. They do manage to help Teyla pull a victory out of her suicidal battle plan, but on the whole, their assumptions come very close to getting them all killed. It's Teyla and her decision to take matters into her own hands (and Todd's timely rescue) that saves the day.
Even with all that being true, did they actually gain anything? It seems obvious, about halfway through the episode, that Todd has been using Teyla and the others in a power play. There's little reason to think that Todd will even honor the agreement to spread the genetic treatment around his alliance. Teyla would have to be willing to make good on her threats, and while she pulled it off in this situation, who's to say that it would be successful in the future? Especially after Todd has been given time to consolidate power in her name?
It's hard to argue that Atlantis is in any better position when the operation is over, and I think that's part of the appeal. The team survived, but things could have easily gone the other way. Even if that is just the "reset button" kicking in again, and even if the tension was resolved a bit too quickly in the final act, it was still a solid outing. One can only hope this is just the setup for something bigger.