It seems they can pick teams based on two different sets of criteria:
1. The top ranked teams with the best records. Under this scenario FSU deserved to be in the final four, over both Bama and Texas.
2. The current "best" teams. This is subjective, and appears to be what they used to justify not picking FSU. I believe they felt that as of Sunday, Bama was a better team at the present time than FSU. It's not really provable, other than FSU being on their 3rd string QB, and therefore not a dominant team. One thing in Bama's favor (I guess) is that their strength of schedule was ranked 5th, while FSU's was ranked 55th.
The problem is that they can pick when they want to use the first criteria or the second criteria, and don't have to justify anything.