Like Dave, I'm very late to Atlantis (watching the episodes on Pick?).
I don't mind delightful Carter being in command (it fits pretty well, I think), the problem, as mentioned above, is that she seems to have sod all to do. If they planned on reducing the leader's role so much they should've given it to a Wolsey-type character who could do the job on screen but whose presence wouldn't feel conspicuous by its absence.
Ronan and Teyla both feel underdeveloped significantly. With Teal'c, after 3-4 seasons or so, you knew he was First Prime, had a son, had a wife, was mentored by Bray'tac, his father was killed by Cronos, he meditates every day, and wild equines could not keep him away from a fight.
Almost the only thing we know about Ronan and Teyla is that they're handy in a fight and their worlds were hit by the Wraith.
I like McKay quite a lot, and Shepherd[sp, I know that's not how the show spells it, but it's not my fault they get it wrong
] has grown on me, but they should've done more with the other two main characters. I know more about Zelinka[sp] than them! [He races pigeons in his spare time and isn't fond of children's parties].