Ideally, an 8, 12, or 16 team playoff would be best, with minor bowl games for non-playoff schools, BUT:
Since it is highly unlikely that the people who control the bowls would just let themselves be "replaced" by a playoff, here is a way that they could co-exist.
1: Let all of the bowls (or any new ones that want to start) continue to exist.
2: Let them make whatever deals they want with various conferences, certain BCS rankings guaranteeing a spot in a "BCS bowl", etc.
3: Play all of the bowl games.
4: Take all of the Bowl WINNERS and put them through some ranking system (it can be the same BCS formula)
5: Take the top 4 ranked WINNERS and place them in the "College Football Final Four"

Neutral Field, 1v4, 2v3, winners play for the NCAA Championship.

All bowls technically mean something, as all winners would be placed in the final computations
More often than not the major bowls would become quarter-final games as those winners will usually be top ranked teams
(but yet in the event a weak BCS conference champ wins their bowl, it's just as likely that a winner of a "non-BCS" bowl would advance to the "final 4")

The final four could even be marketed as: "Rose Bowl Champion" vs. "Sugar Bowl Champion", etc. (to allow the bowls to maintain an identity apart from being part of a playoff...