If you raise the age limit, more players will take the Brandon Jennings route of playing overseas until they are eligible.
Create a financial incentive for staying in school. Players under the age of 21 who have played less than three years of college have an addition year of restricted free agency. Have the rookie scale contract amounts include a 5% bonus that doesn't count against the salary cap for players who complete college.
This will probably create some incentive for teams to draft teenagers who they get to own for less money for a longer period of time, but that may be balanced out by players having a disincentive to put themselves in such a situation.
One reason that baseball and hockey have minor league affiliates is that those minor leagues were originally completely independent of the "major" leagues and later formed affiliate relationships. Football just requires too many players, so minor league football takes the form of arena football, while the NBA never went beyond negotiating the allowance of ten-day contracts in its relationship with the CBA. The NFL did try to build a farm league with NFL Europe, but failed.