Here is the five things I would love to see changed (in order of importance):
1. Change the way fouls are both determined by the engine and assessed to individual players. - All too often I see teams that have more athleticism, speed, and defensive skill rack up more fouls than their less athletic and slower opponents; also, the seemingly random nature by which individual players are assessed fouls...having your best all-around player (or excellent defender) spend most of the game on the bench for the stupidest of fouls can kill your season.
2. Have the option of selecting individual defensive match-ups if you run a man-to-man defense.
3. Lower (or eliminate completely) the disparity between lower and upper classmen. - Juniors and Seniors are already going to typically be better players because of their time to improve, but this is not always the case and punishing players simply because of what class they are currently in seems rather unnecessary.
4. Changed the way Scouting Trips work so that coaches can choose one skill that will be among those listed in the corresponding scouting report. - Having to spend $1,500 just to find out a players level of potential in ball handling can be maddening, and not to mention could possibly be risky/detrimental at DII & DIII given the relatively little amount of information you gain at such a large price.
5. Change the end of game logic so that (a) your best shooters or scorer take the most important shots when playing from behind, and (b) so that your best free throw shooters have the ball in there hands when a team has the lead and the opponent is fouling intentionally.