There are a few things I would change that aren't rules per se, but changes I would like to see nonetheless. The first would be to allow the official scorer to decide who the winning and losing pitchers are for each game. It just doesn't seem right that a starter could pitch 8 scoreless innings, the closer comes in and gives up the lead and if his team scores in the next inning, he gets the win.
Another one is if a fielder madly misplays a ball, it should still be considered an error even if he didn't touch it. The batter shouldn't be awarded a hit if a popup lands in between 3 fielders in front of home plate.
I realize these aren't exactly rule changes and would have no impact on the actual game, they are still things that should be changed.