I doesn't matter how or why the system is inconsisent, only that it is. There will be another instance down the road where there will be three (or more) undefeated teams at the end of the regular season and conference championship games, and thus one or more teams will be pissed off because "the system" screwed them over. You put a 16-team format in place, and no one will give shit about how #17 thinks they got screwed out of the playoffs.
I'll try and get back to this and avoid the trainwreck if I can.
This is the reason why I feel you can do a 1A playoff with just the top 8 teams. I could see the possability of teams ranked 8-16 still being able to win it in 1AA or DII but I just don't see a #9 team having much gripe in D1A.
Here are some specific examples as to why I feel this way based on the final BCS polls the past few years.
2004:11-1 Boise St would have been the odd man out.
2003:11-2 Miami FL is BCS #9.
2002: 10-3 ND is BCS #9
2001: 9-3 Stanford is BCS #9
2000: 9-3 KSU is BCS #9
1999: 10-2 MSU is BCS #9
Just like the NCAA basketball tourney the griping would have lasted about a day from anyone of these teams in these years. The gap between the top 5 caliber teams and the rest of the top 25 teams is much more significant in D1 football than any other sport imo and thats why I feel 8 teams is enough to settle it during any given year.
Also the seeding concept with home games to the higher seed would finally take away a hugely unfair advantage warm weather schools have had for decades.
Also, in my world you start the playoffs the week after the CCG's and with only 8 teams you can have the NC game in the Rose Bowl on Jan 1st every year the way God intended it to be.
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I hate the wild swings in performance the month off produces, even if our coach takes better advantage of it than most.
I don't feel you are seeing the same teams you saw all season long in Bowl games and eliminating the big time off lag would ensure your just seeing the best 8 teams you've seen all year settle it on the field once and for all. Maybe work a week off in there if you can and if i have to make sacrafices to my plan this would be the easiest one for me to give or take but in a perfect world for me there is no December long layoff.