That's a problem too!
Even factoring in some at-large bids, what will the #14-ranked, 10-3 <insert team here> feel when they don't get a spot in the dance, and have to watch Miami (OH) go in their stead?
They should feel that they should have won their conference.
If 12-0 Nebraska beats 12-0 Ohio State in the Big 10 Championship game, then Nebraska goes to the playoff. Sure, Ohio State will be upset they're not in the playoff, but all they had to do was beat Nebraska. Then Nebraska gets a #1 seed and plays Miami (OH) in the first round in Lincoln, and Miami (OH) wins. Well then, Miami (OH) did what Ohio State couldn't, and they move on.
In a scenario like that, Ohio State has no room to complain. Win your conference, earn a playoff berth.
If instead you use polls to award playoff berths, you're making conference championships less meaningful, and even less desirable. Look at 2010. Because of the reactionary nature of the polls, teams who lose later (including in conference championship games) get hurt more. In a 16-team playoff, Nebraska would have been a shoo-in before the conference championship game against Oklahoma. However, after a loss to Oklahoma, they would have dropped out of playoff contention, and Missouri, who lost head to head against Nebraska and couldn't even win their own division, would be in the playoffs. All because they lost their division, and therefore didn't have to pass the extra test of a conference championship game. Nebraska would have been punished for their regular season success. How does that make any sense, and how is that fair?
The influence of the polls should be minimized as much as possible - they're crap. Use them to seed teams in the playoff structure, nothing more. Playoff berths should be decided on the field, and the only way to do that is to grant playoff berths to conference champions.
Yeah, poor #5. But that's the controversy part that is inevitable to college football! It's essentially poor #3 now, but poor #3 has been an undefeated BCS conference team in the past. I don't see that happening if we go to a Final Four, and if it does, that's too bad. You can't bend much more than four. Because once you do, it's not Poor #9 anymore, it's Poor (5 semi indistinguishable top 15 teams). Or (15 indistinugishable mid-range teams with 9 or 10 wins apiece). And so on.
Also, it's never going to be that teams #1-#5 are all undefeated. But teams #1-#2, or #1-#3 will be undefeated, and teams #2-#5 or #3-#7 will all be one or two loss teams from major conferences. 2-loss Alabama will say they're more deserving than 1-loss Boise State, and 2-loss Ohio State will say they're more deserving than 1-loss TCU.
As stated before, the only way is to minimize the impact of the polls. They suck.