The prestige system that currently exists makes it impossible for a coach to build a powerhouse out of a real world also-ran team. You can make a good run but the baseline will always pull you back. My time at Army is a great example of what the system is designed to do - prevent non-BCS teams from establishing a dynasty. Considering the name of the game, it's pretty ironic.
There is some merit there because it accounts for a lot of the issues we don't deal with in this game (budgets, arenas, facilities, personnel).
The downside is the only real jobs a coach can be successful (at a national level) in the long term are centered in the top conferences. The story to be told is the one WhatIf wants told. We can't write our own. You either accept that or leave the game. I'm playing out the rest of my pre-paid seasons to see if their story is as much fun as the one I tried to write.