The biggest reason there probably isn't a minor league system in football is cost. The blue bloods of college football are like a defacto minor league system that is costing NFL owners basically nothing. If they did set something up like MLB or NHL they would have to pay these guys and also foot the bill for their development. Can't see them doing that when someone else is doing it for you. The only real advantage they would get in a minor league system is they would own the rights to the players.You're absolutely right. Some things definitely need to change. The 3 and out rule is probably just the first of many.
A "minor league" for football could and should be established. Works for everything else, why not for the NFL.
Makes college football like what baseball, basketball, soccer, and the rest were always meant to be - amateur athletics by true student athletes.
The only problem I see with what you wrote is really towards the end. I could see a team like Florida who can't out-recruit Bama but decides to simply outspend them. Brings in a "mercenary" team of former NFL career backups for example to come in, spend a semester, and win a national championship, which would be what I could easily see happening if allowing former pros to come to college. Even though they're all backups, they're still much more mature, stronger, faster, and have a much smaller learning curve than the typical true college athlete- even the ones at Bama. Personally, I wouldn't care about it other than the fact it would be a true safety issue. Same thing basically as allowing high school players to play midget or junior high ball.