The “Siege, Part 3” wrapped up everything, but I didn’t fully like the nuke-over-cloaked-city trick. Atlantis was the last refuge and was submerged as the Ancients left. So why wouldn’t the Wraith have continued attacking it and destroyed it or infiltrated it over the years? Similarly I wouldn’t think that even the Wraith would be fooled so quickly. At least stick around and see if anything important surviced, if there were people who evacuated over the ocean, etc.
Technically, it seems hard to believe that a small Jumper’s cloak could be made to cover a large city. The city would at least have to have projectors for the cloak. It would also seem that the Ancients would have thought of this before.
As for McKay, it doesn’t make sense that the Wraith waited until he drew his sidearm and tried to fire. It would have been better if he had talked to himself behind the crate, steeled himself, and then jumped up and fired at the same instant that Teyla did. McKay’s bullets could have fallen and then the shot Wraith could then have fallen at McKay’s feet.
I liked that Weir and Sheppard shared a similar concern as each thought the other had died. A good development of their characters.