Take the champions of each conference and have playoffs. Simple, no frills, no debates. Once you're down to the final two teams, they play and you have a national champion. Of course, Notre Dame and the other "independents" will cry foul, the Big Ten Commish will be vehemently opposed when his conference's champs go out in the first round, but that's why they're called the playoffs.
You would probably have to cut the regular season to 10 games, but I see no harm in that. Bowl game organizers would hate the idea, but that's something that could be sorted out if and when a true playoff system was arranged and implemented. The ONLY thing the BCS ratings should be used for is tie breakers within a conference. For instance, after tonight's debacle in Norman, there are 3 teams tied for 1st in the Big 12 South division......who will represent the South in the Big 12 Championship game will be decided by the last BCS rankings, barring a loss by any of those 3 teams.
Just my 2 cents......