Major Thoughts:
Allocation Draft and Free Agency: Guys 5 years or younger (accounting for the redshirts) are the only ones eligible to be picked.
Free Agency: Only in the offseason, unless major injury concerns are happening. Free Agency could simulate the "walk on" process.
Trades: Likewise only in the offseason, max of 1 player (because you're always going to have that one guy that might want to transfer). The trade -has- to be for a Draft pick (to simulate freeing up an additional scholarship), and as equivalent as possible.
Releases: Probably the toughest part. We could probably simplify it to just release 4 and 5 year players at the end of the season, or set some sort of career threshold stats that force a release.
Minor Thoughts:
Coaches: Coaches usually don't get poached, so that probably shouldn't happen.
Rivalries: Rivalry games should be towards the end of the year, as they are in reality. I.e., I'm looking at "The Big Game" being the second game Cal and Stanford play this season. If there's a home field consideration ("The Big Game" alternates: Odd years at Stanford, even years at Cal), maybe take that into account as well.
Not sure what else... Just initial thoughts.