It's purely a numbers game/problem. In order for it to work effectively, you'd have to be able to more accurately project a kids ability coming out of high school, and that isn't going to ever happen IMO because people physically and mentally mature so differently from one another.
What % of CFB players get a shot in the NFL? Maybe 1-2%. There are 120 some D1 CFB programs with ~100 kids on each team, and the NFL takes ~225 draft picks every year (from many different levels, schools and backgrounds). CFB teams need that many kids on each team because frankly, a lot of kids are not physically mature enough, or don't have the skill level at 18 to play against a 22 yo senior. Or they just aren't what you thought they were when you recruited them, and they wash out. To get anywhere close to the quality of player out of a minor league system that you get out of CFB as a whole, you would need to invest heavily in scouting, and put a TON of kids on each team so as to allow for, time, maturity and development to separate the "cream". To me, this means the minor league would need to dilute the financial incentives to each player in order to allow for it to make financial sense. Maybe pay each kid $20-$30k a year to play football? Because you are going to have WAY more misses then hits, and money paid to a "miss" is a throwaway.
Who is going to buy tickets to go watch these kids? What happens to the kids that wash out? How does anyone with financial sense invest in such a model? Honest question....I just don't see it working.
College football does all of this, and gives an opportunity for a college education to the 98-99% that don't make it. The problem with college football is they don't take care of the product well enough due to the archaic NCAA rules, and there is far too much disparity between the haves and the have nots. But there is still plenty of NFL talent that comes from "lesser" recruits and from smaller schools. You have to have the volume in the feeder system to keep the NFL product quality. The way it works now is best for everyone, except for that the people without a seat at the table (the players) are taken advantage of so that everyone in a position of power can reap a disproportionate amount of the benefits (Coaches, AD's, Conferences, NFL, etc...).