"Missouri and A&M would have made a lot of noise in the B12 that year" - There is absolutely nothing but opinion to support that. You fell into the trap that I outlined - that people automatically assume the SEC it so awesome. The fact is, aTm and Miss were middle of the pack and it B12 and near the top in the SCE one year later. In that same year OK kicked the trash out of Bamma in the Sugar Bowl and FSU with their #64 SOS beat Auburn in the NC game. So the actual facts don't support the OPINION that the SEC was the best conference in football last year - Quite the opposite. The SOS argument also gave us Bamma vs LSU when they had already played and OK ST was fantastic that season but never got the chance. It gave us Nebraska who wasn't even good enough to make their own conference championship game - and the proved it in the BCS championship game, and several other gems over they years.
Boise, TCU , Utah (Choke) and maybe even BYU would have been able to beat any of those teams on any given day but they never got the chance because their SOS wasn't good enough. Yet somehow FSU was good enough even though their SOS was worse than any team's SOS from the hay day of the MWC. It was on par with BYU's schedule this season yet the talking heads had discounted BYU when they were 4-0 because of SOS (which was 15th in the nation at that time).
As I said - there is not even close to enough data in a 12 game schedule to measure SOS. It is even subjective in a 30 game basketball schedule. You yourself said that the "southern teams" were all that even though the results on the field didn't support that opinion.
The only true way to measure it is to prove yourself against your conference for the chance to prove yourself against everyone else. That is the way to get a true champion. SOS and rankings is gymnastics scoring.