Loved this in NCAA 13, but removing the WAC really hurts. I was planning on something similar, but having only two Tier 3 conferences (fed from each pair of Tier 2 schools) and leave FBS Independents by itself with only 2 schools in it (worst of the worst). The one weakness with last year is that since it isn't a "real" conference, the schools never played each other, so determining a winner was kind of arbitrary.
That's how I did it, though I think others went by highest ranked from each conference in the national polls. JoshC1977 did update this for NCAA 14.