1. Title IX effectively makes paying the athletes outright a non-starter. Only a handful of university athletic programs (~20 - 30) have enough income to pay all athletes an equal salary that is more than a token stipend.
2. Third party likeness agreements are one way out of that sticky problem, but they are really going to have to monitor it closely. I'd like to see how they approach things like caps, who can actually sponsor the athletes, and so forth. I worry that Jim Bob's Chevy Dealership in Daphne, Alabama and Doug's Night Club in Houston are going to, effectively, make Alabama and A&M real professional sports franchises where they can afford to pay their back-up DE $100,000/year. There are three major potential issues with this:
A. It would wildly exacerbate an already obscene level of inequality in the major sports.
B. It would siphon off a fairly large chunk of marginal income that the university already gets above-board in donations, ticket fees, etc. This would have pretty serious effects on non-revenue sports.
C. Related to (A), the value and potential income for the mid-level and low-level programs (think mid-level P5 down to high-level G5) would take a serious hit. Fans might think they have a long shot in football or basketball right now, but if they knew with certainty that it would never happen no matter what because of what are effectively salaries, then those programs are going to seriously hurt.
3. Most of the value in these sports is tied up in the brand itself and not the athlete. With very, very few exceptions (Manziel, Newton, etc.), fans care much more about the brand than the athlete - on a scale of 0 to 100, the value tied up in the brand is probably 90+ and the player less than 10. Contrast that with, for example, the NBA or EPL. College football, in particular, is a brand-loyal sport and not an athlete-loyal sport.
If you could get rid of Title IX or somehow separate revenue-generating sports from non-revenue generating sports in that equation, it might help a bit. If you could ensure caps or have a standardized and approved list of sponsors, that would again help. They are opening a big ass can of worms here that is going to result in a difficult beast to tame.