Something that just came to my mind (that might be useful all-around) is the ability to do... Well, for a lack of a better term, a "virtual scrimmage" against another team in the league.
Say for instance, I know I have a game against Pittsburgh in a few weeks, and I want to see how I'd fare, where my weaknesses are, etc., so I can be prepared to gameplan and shore up holes when I actually -do- play them. So I can sim a game against them, with full gameplay and stats, to see where my team might need improvement.
I could see this also being useful as a 'developmental tool', to see where some of my rookie talent might be ready for the big-time despite their ratings, or what veteran might be ready to falter.
I could see this most easily being implemented during the midweek portion of the sim. Give us the option of 'simming' a 'game', and it'll run separate but alongside the rest of the sims run for the other leagues during that time period. Obviously stats won't count towards the actual league, so have a separate "practice sim" flag set for those ones, so that stats, injuries, win/loss, etc. don't get added into the league.
It could be a step in the direction towards the practice squad setup I've seen mentioned before, but it already uses the established rosters and sim engine. The big things that would have to be 'copied' would be having separate gameplans, depth charts, and possibly coaching options for experimentation purposes.