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also, Marshall and TCU went 11-2 and 10-2, and won their bowl games, but didn't even crack the top 20

Your whole argument is fair except this deviation. When a team like Marshal schedules nobody and beats up on nobodies, then loses to Akron (Leftwich or no Leftwich or injured Leftwich, no excuse) they do not deserve to be considered for a National Championship, regardless of record.

Fair enough. I'm in Muncie, home of Ball State (also in the MAC), so I'm probably prejudiced. ;^)
But Marshall had a decent run with Chad Pennington. IIRC, they finished #11 and trounced #25 BYU 21-3 in their 2001 Motor City Bowl. While it's not fair to include a 12-0 team who only beat patsies, it is also unfair to hold a weak conference's 12-0 team out simply because they didn't schedule tougher opposition two years in advance.

Okay, here's my update: the weaker conference teams have to go undefeated to get a potential wildcard invite to the Elite Eight... TCU and Marshall this year wouldn't qualify, but Marshall in 2001 would... and as long as there are no other worthier teams (like Texas this year. It hurt me to not include them in my top 8. I guess I could bump Boise St since they lost that one to Arkansas, heh-heh.)