Bison, assuming we're doing away with the BCS, who then constitutes the non-BCS conferences you're referring of? And if there is such a clear division in talent, why need a playoff at all? Simply allocate the two best teams going to a championship, since obviously we'd all be able to tell based on their conference and performance.
Oh, wait. That sounds familiar...
The fairest way would be to have a 117 team playoff at the end of the season. But obviously that's not possible.
What then becomes the fairest way?
Obviously a playoff.
How big? 8 is too small, 32 is too big. 16 seems perfect to me.
Which 16 teams should get to go?
You say that if a team wins a conference, regardless of how weak that conference is, they should get to go?!
That's not fair to teams that are better but play in tougher conferences.
Obviously, the fairest way is to have a ranking system and send the 16 best teams to the playoff.
Bottom line: unless we can get a 117 team playoff at the end of the season, someone is always going to be left out.