I don't know if Utah was the best team in the country but with the current system going undefeated and defeating Alabama (a team that Florida barely beat) convincingly, they should have got a share of the title.
Utah got screwed, IMO. if they weren't in one of the worst conferences in the FBS, then i am sure they would have gotten AT LEAST a share.
I'm not a fan of the BCS, but the logistics of a basketball-like playoff system in football wouldnt really be practical either. I'm sure everyone would complain about only allowing 8 of the teams in to a playoff system. Or even 16. How long can you extend that season? But then again, having 8 or 16 teams battle it out would really determine a champion on the field.