One rule I would like to see changed is the balk. I personally feel it adds nothing to the game. If your team is on the benefiting side, it's a no-skill advantage; it just feels like a cheap unearned base. If your team is on the offending side, it feels stupid and annoying as hell. Most of the time, it's just a tiny flinch, and without replay (e.g. when you're at the ballpark) there's no way you'd know it happened. All in all, it seems like a very nit-picky technical rule that is the opposite of exciting.
I do think you still have to have a balk rule, otherwise runners wouldn't stand a chance. However, in my ideal baseball rulebook, there are no automatic bases for balks. Instead, if a pitcher balks and a runner is picked off, that runner is called safe instead because of the balk. If a runner tries to steal and is caught after a balk, the runner is safe. And the 9/10ths of the time a balk would make no difference, play just goes on, as it should. Runners would still be able to go on first movement towards the plate, pitchers would still be held accountable. And the game of baseball would be better.
Bonus Rule Change - Retractable Roofs
Another rule change I want is that the home team *always* gets full control over when to open or close their stadium's roof. I'm sick and tired of the league dictating the state of the dome in playoff games </rant>