When it was evident that the BCS was here to stay, I was a fan of a plus one--pick the best 2 after the traditional bowl games and play that game at a neutral site. Sure would have cured the Washington/Miami, Nebraska/Penn State, Nebraska/Michigan, LSU/USC problems.
But other years (Nebraska-Florida, USC-Texas), it would have been messier, although I guess you are saying those teams wouldn't have played. In 1995 Nebraska would have gone to the Orange and Florida to the Sugar, and if they had won, then would have played after that. Same in 2005 with Texas to the Fiesta and USC to the Rose.
I still think 8 is probably the right number. I always liked the 6 BCS champs, and then 2 best at large. Then when the Big East got raided, I thought 6 best conference champs. Then I went to 5-3.
But either way, I wanted to quarterfinals to be the existing tie ins. Rose was Big Ten champ vs. Pac Ten champ. Orange got the ACC champ, Sugar got the SEC champ, and Fiesta got the Big XII champ. Those 3 were seeded, and played the other 3 teams (Big East champ, At Large #1, At Large #2) in seeded order. Avoiding conference rematches
So for example, in 2003 (the last year before the Big East was neutered)
ORANGE - #1 Oklahoma (AL) vs. #7 Florida State (ACC)
SUGAR - #2 LSU vs. #9 Miami (BE)
ROSE - #3 USC (P10) vs. #4 Michigan (B10)
FIESTA - #5 Ohio State (AL) vs. #10 Kansas State (B12)
Then the 4 winners are paired based on seed. Is it totally fair? No, but I think its a solid balance