The two that stick out to me like sore thumbs are Ball State and Marshall in the Big East...unfortunately, there's pretty much no firepower left in the non-BCS conferences to replace them with.
The nicest thing about all of this is that I'll be able to make yearly changes to keep things nice and balanced.
One thing I am considering is moving Penn State, Notre Dame, and West Virginia into the Big Ten, Tennessee into either the SEC or ACC, and making the Big East a nine team non-BCS conference with six independent schools. If I can completely get rid of the independents, then I can make three 16-team BCS super conferences, and eight 9-team non-BCS conference.
Something else to consider would be two super conferences (16), two BCS conferences (12), and seven 9-team non-BCS conference with one independent school.