Oddly enough, the two teams who met for the 2003 title play in the only two conferences who hold league championship games -- the SEC and the Big XII. LSU beat Georgia in the SEC title game, while Oklahoma was drilled by Kansas State in the Big XII title game but qualified for the Sugar Bowl thanks to its commanding lead in the BCS rankings.
Even though Oklahoma and LSU survived league championship games to play for the national title, the current system is unfair. It's not right that an SEC team or a Big XII team has to play an extra game en route to the national title. Either every conference should hold a league championship game or none of them should.
Personally, I'd like to see conference championship games dropped and a playoff system implemented involving the four BCS bowl winners. This way, the two playoff finalists would play 14 games each, the two semifinal losers 13 games each. The other bowl teams would play 12 games each and everyone else just 11.
This system wouldn't eliminate the bowl games and it wouldn't extend the season significantly. Best of all, it wouldn't leave half the country recognizing Southern Cal as national champ and the other half recognizing LSU, as is the case today.