I think the current system raises the most concern in fans who enjoy the off-field banter more than they enjoy actually watching football games. The fact that a team is out of national title contention doesn't void the rest of their schedule. Yes, for some, the number of 'important' teams left dwindles, but importance can be found beyond a national title shot.
Will Iowa ever win a national title with the current system? Not very likely at all. But if I could go back in time and institute a playoff for the 2002 season, I don't think I would. Those Hawks controlled their own destiny from day one of summer practice, just like most other teams do. That ride was magical nonetheless, and I followed every second of it, just like I followed every second of 1999 hoping for one Big Ten win. That's where the heart of college football lies for me.
Do I care that Boise State and Alabama didn't play in 2009? No. If I had my way, we would be in the original system and whoever wanted to crown them and hand them a trophy could. Then you have two schools with all-time cherished squads and perpetual bragging rights, not either alternative (an exposed/deflowered Boise or an utterly embarassed Alabama). I just don't see the need to perfect a game that is perfect in its imperfection of often, but not always, awarding perfection. Therein lies the magic.