I have seen the same thing with my created coach using Texas State. I think the biggest issue is The bigger schools do not have certain advantages that they have in real life. The biggest advantage in real life is having larger budgets giving them the ability to recruit more players than smaller schools. In the game basically all schools have 5000-6500 points to spend each week, which causes the Big schools to fight each other over the coveted recruits and unable to put any points into the second tier guys until the top tier guys are gone. This leaves the second tier guys open to the smaller schools, the CPU smaller schools do not take advantage of this like a user can.
The bonus points for bigger schools are usually higher but 100 points or so more a week doesn't make up enough points when a small school is over 1500 points ahead with 3-4 weeks to go.
Bigger schools need to have larger budgets, in many cases almost 2 times the amount of points compared to smaller schools. This would make the 4 star guys harder to get for smaller schools. it would allow bigger schools to not only battle for the top tier guys, but still able to go after the 2nd tier as well.