On the field: Really the sport has roster rules exactly backwards. Start the minor league season LATER. You really should have your 40 man roster in April, not September. Go to automated ball-strikes calls. Umps are lousy at it, it's an impossible job for humans to do. Also - the strike zone is in the rule book, that umps interpret it their own way is a mistake.
Off the field: Allow trading draft picks. (Hell, abolish the draft - but that's never going to happen) Abolish salary limits. Get rid of draft pick compensation for free agents.