I loved the intro - flying monkeys! And then John talking to Woolsey about the flying monkeys. And Woolsey's expression!
The malfunctioning jumper was such a surprise. From the promo I knew that Fran/Weir would come back but this was a huge surprise. And so suspenseful too! That was something very unusual because on SGA, the jumpers never fail!
I liked Weir in the computer thingy and John mentioning Ava! Nice continuity. And I did understand why they were so distrustful of her, no matter how much they wanted to believe that it was her. I loved what John told her, that she might think of herself as Weir but she's not Elizabeth anymore. The look on her face then...
Woolsey was awesome in this episode, a real leader. He made the hard decisions and no one could blame him because they knew that he was right. For once, he and Ronon agreed on something. It was really nice to see him actually be the commander of Atlantis.
What I didn't like was how everybody kept harping on Rodney to find a solution right now. Like he's some sort of "Insta Miracles Rodney". On the other hand, it's partially his own fault - when Radek offered help, he snapped at him and sent him away. And then, of course, he didn't manage to complete the program in time.
The ending was sad. Really really sad. I loved the camera centering on John, the sad look on his face.