They should play more so they are ready for the NFL? Seriously, you have like 250 guys get drafted out of like 10,000 D1 college players. Plus, these are student athletes. Its not like they have nothing else to do but play football. Last note, these guys play a schedule much closer to their pro league than any of the other major sports- NBA, NHL and MLB. If anything you hear the hitting the wall in the NBA more than NFL.
Your second point might be dumber than your first. Why wouldn't the NCAA complain about injuries. Sure injuries can happen any play but more plays means more injuries.
Under your plan why not a 64 team playoff? Players would really be ready for the NFL then and injuries can happen anyway.
16 teams playoffs can likely only happen if you limit the regular season games and/or title games more, its that plain and simple. With a conference title game and the national title game your talking 17 games total. I don't see that flying with the NCAA. In D1A- i believe 15 is the most you can play.