I'm all for Woolsey taking over. Him coming in and being a bastard and not getting along with every single member of the expedition is what the show needs. Otherwise you end up with something like Star Trek Voyager where everybody works together to solve the problem of the week and then congratulates each other about what a great job they did. It gets stale really fast if everyone on a show is a 100% team player who never has a problem with anyone else.
Or put another way: Who is the more interesting character?
Caldwell and Ellis or all those other agreeable and cooperative ship commanders (who always end up getting killed.)
Wraith enzyme Ford or season 1 Ford
Daniel Jackson or Jonas Quinn
Kinsey or Hayes