Take matter into your own hands, control a team in the Big Ten that you play and beat on of the teams that get the unfair advantage. Ensure that the big time schools can't use their past to get ahead of you in the now (or rather 12 years from now). The SEC always gets a boost after their championship game even if they beat a #24 team with a 7-5 record in the game so if there is ever an SEC team ranked #3 control their opponent in the SECCG.
Make sure that patsy is in a good conference though, or since it would appear you are good enough to beat most teams don't bother doing the patsy until you are no longer getting screwed by the rankings etc. And make sure you SPREAD OUT the times that you play these teams. If you schedule all of your big opponents in the first couple of weeks you won't be able to compete near the end of the season when top teams are playing other top teams within their conferences.
quick question what was Purdue's Academic Prestige rating when you started the dynasty? For some reason Georgia Tech's rating is 4 Stars despite it being consistently in the top 10 among public schools (hovering around #7 over the past couple of years) and it is right up there with MIT in terms of engineering, how is that not worthy of a 6 star rating?!