Yeah I read that yesterday. To be honest I'm not surprised that they didn't leave Carter in command, I love her on the show but Atlantis is missing that )(Civilian"/SGC conflict that sg1 had. With a member of the NID in charge, i think we are about to see that conflict come to a breaking point.
I think they can trust Richard Woolsey, but not so sure about some of the people in his organization.
With him at the lead I'm sure the NID would LOVE backing a proposal that would maybe add some new teams to the expedition.
I remember a scientist in the ep where John got bitten by one of those wraith bugs and the Jumper got stuck in the gate in orbit... Lets face it they're are a few people who don't like the way Atlantis has been run up to now and with a member of the NID in charge I expect to see a lot of strange things happening.
Beware our Trust.
