1. Restrict maximum AA budgets to be proportional to the number of student athletes. Alabama and Oregon don't even know how to spend all their athletics money, and yet they have mediocre academics. I would restrict the maximum amount of $ an AA can spend (after tuition and housing for athletes). Something like $50k per athlete. Need to spend more than that? That's fine, but for every $1 spent over the limit you have to give $2 to the university to support academics. Want to build a giant athletics complex to attract recruits? That's fine, but then the university also gets to build a new physics building and library. Want to pay Saban $10 million? That's fine, but then the university gets to give every faculty member a $30k raise. You have to be an excellent academic institution FIRST, then you can be an excellent athletic institution. What would this do to college athletics? Well, many coaches would get pay cuts, so there would be a coaching migration to pro sports. That's fine.
2. Require all DI athletes to have a combined Math+Verbal SAT of 800. That requirement also applies to all transfer students (JUCOs). Throw out GPA, just require a high school diploma or GED. Does 800 sound low? Consider that the current NCAA minimum is only 400! A score of 800 is the 14th percentile. Maybe make it more flexible than that to account for students who excel in one subject over the other, like if you get 500 in one or the other then the total can be lower. Currently, high schools are fudging the GPA to get low-performing students eligible, and they think they are doing them a favor. In reality, they are set up for failure in college. That doesn't stop colleges from keeping them eligible, they just cheat as well, see UNC. What does that do for athletes who don't make it as a pro? Well, kids are graduating college unable to read. Seriously:
http://www.cnn.com/2014/01/07/us/ncaa-athletes-reading-scores/
http://deadspin.com/5223328/ole-miss-football-players-dont-read-so-good
http://www.nytimes.com/2008/12/12/education/12kemp.html
If student athletes have to actually learn stuff in high school to be able to play in college, perhaps high schools will actually teach them. Then maybe colleges wont feel the need to cheat to keep them eligible. Also, lobby the college board to tighten up SAT security. It is not that hard for prospective athletes to cheat to gain eligibility. Maybe require fingerprints?
That's about it. This system would maintain the focus on academics, and would be in the best interests of the students. If a school doesn't like it they can leave the NCAA. I can see it now, a minor league consisting of Bama, LSU, UGA, Auburn, Tennessee, UGA, Florida, FSU, Clemson, Penn State, Ohio State, Texas, Oklahoma, Nebraska, Michigan, USC, Oregon, etc.