I have two suggestions that would dramatically change the game closer to RL. One is a lot easier than the other.
First, if a runner is not held on 1B, his chances to steal have to go way up. For Example, a Tim Raines 50/55 in SB is probably automatic if not held on. I have seen too many times where strong arm catchers have good success against great base stealer who are not held on. We all know anyone with decent speed not held on is going to steal 2B a large %.
Second, the BBs in this game continue to be a joke. My understanding is the rules engine evaluates the batter first to see the hit/out. In my opinion only, the #1 determinant of BBs is the pitchers ability to throw strikes. NOT the batters eye. Barry Bonds is a joke. A large % of those BBs in RL were because no one hit behind him and pitchers IBB or pitched around. If Babe Ruth were hitting behind Bonds, his walk total would have been much less. Probably a hard fix.