I love the way you've turned this around so that the Tau'ri are the strange aliens (as it should be) in Atlantis and the Pegasus locals are competently handling the Wraiths. Ronon is the one in charge and John has switched places as the most junior of the group. Fascinating to see how that changes John and makes him sulkier, more socially isolated. You gave hints but I'd've liked to see more of Elizabeth. I have the feeling that her skills would be absolutely necessary in this AU.