But he didn't unexpectedly take over the show eventually. He was only unexpected in the casting process. By the time we were watching (ie, the pilot episode), he was one of the stars that we were ALREADY familiar with, right?
I don't think it's possible for main stars to take over a show they're already a main star on, really. A better Atlantis argument might be Zelenka or Lorne since they started off as more background characters, if they had only used them more instead of keeping them so secondary.