Ron and Dave allude to what they had planned a little bit on the podcast for You Can't Go Home Again - at the end they talk about how much they love the Kara/Adama relationship and that how there was a storyline comming up where they were going to put her in charge of the "thingy" (since the Pegasus was still a spoiler at that point) and how she would be interacting with Adama and challenging him in new ways. I think that would have been really interesting - I guess they tried to do that with Lee and Adama, but the fat!Lee thing ended up swallowing (no pun intended) Lee's command storyline IMO.

It would have been fun to see how her relationship with Adama changed. Season three would have been so different, at least in the beginning; I imagine she couldn't have mustered out, and they couldn't have put her on the self-destructive track after having her rise to such a strong leadership level. No captivity with Leoben. I guess she still would have had to fulfill her destiny, but I imagine it would have played differently.

Though there is the obvious question (which was Jamie's question!) of why not Lee. Maybe he would have taken longer to recover from his gun-shot wound, or Adama would have thought he was needed on Galactica. I think if not for Lee, Kara would be the next logical choice; Adama would never have put Tigh in command voluntarily , I don't think, especially not after what happened once he was shot. (And Tigh wouldn't have really wanted that).

Definitely an AU with a lot of potential. :)