re: Can we just talk about how Florida State was completely out of place?

I agree, but they went undefeated in a power 5 conference. They did everything required of them to be in the playoffs. With the BCS, they would have been the #1 seed. Would their defense have matched up as poorly against Ohio State's offense as they did against Oregon's?

Would Alabama have been more equipped to handle the Ducks?

We very well could have had a completely different result.

#1 Florida State vs #4 Ohio State
Florida State's defensive line is much more readily equipped to stop Ohio State's run game than was Oregon. Also, Florida State's red-zone offense would provide more matchup issues for Ohio State's defense. FSU could win this.

#2 Alabama vs #3 Oregon
Alabama's defense and running game would have done exactly as Ohio State's did. Alabama pulls away late for a 2 score victory.

#1 Florida State vs #2 Alabama
FSU actually is not the big underdog one would imagine in this one. Florida State certainly has all of the tools to remain in striking distance late in this one setting up a potential late game-winning drive by Famous Jameis.

It's all about the seeding.