My idea for a rule change would be for teams to be allowed to trade draft picks. This would really add to the appeal of the draft and make it more interesting. It would also allow contenders to sweeten the pot a little in trades. The issue is that the guys are so far away from actually making the show unlike in hockey, football and basketball that teams may not trade up for a prospect they like as much or that prospects are at a much higher value because of this.
If I were to do a rule change on the field it would be that the ump would have an earpiece where someone could tell him whether the pitch was a ball or strike. This would eliminate bad calls and also keep the umps in the game. This also could speed up the game so players/managers don't come out to yell at the ump