In the end - the NCAA will follow the dollar trail... It's really become disgusting...
When there were just two teams, people complained about #3 and perhaps #4 being screwed and they complained about polls, computers, and secret formulas.
Now there are 4 teams, we're seeing complains about #5 and #6 (although 5 did beat 6 head to head in a basketball like score of 61-58). There's also complains that the "select(ion) committee" could be biased or didn't have representation (Big12, Baylor coach comments). We also see the media hyping up certain schools - the media from stations that pay the NCAA a lot of $$$'s - think about it.
If we go to 6 or 8 or 16, there will always be complaints about some team being screwed. Think about basketball - there were 64 teams... Complaints trickled in and they created a 64 v 65 "play in" game.... Seeing how much money they made off of that there's now I think 4 play in games (like any of them have a snowballs chance in hell of winning).
The bowls won't go away - too much money to lose. I do wish they'd stop messing with New Year's Day bowls - now they're spread out over two days with virtually no overlap other than Outback, Cotton, and Citrus. The Fiesta and Orange on New Year's Eve... Really? I'd prefer the clicker in one hand and changing stations to avoid the commercials or poor matchups resulting in blowouts... Oh and by the way - other than one bowl (Sun Bowl) all games are on Disney owned stations - hmm... where's that money trail again?