If I was commissioner, here is what I'd do.
1) Eliminate replay during the regular season. If they blow a call, who cares. It's one of 162 games during the season.
If I have to have it, I'd institute a 15-second decision clock. The manager had 15-seconds to decide if he's challenging. What we have now is idiotic. There basically are 4-5 unofficial challenges in every game as the manager waits until his own people watch the replay to decide if he's going to challenge. My decision clock would be put the impetus on the runner to not BS the manager. He should know if he was safe or not.
2) Make the foul poles way higher or use some sort of technology (laser?) that instantly tells me if a home run was fair our foul. There should be no doubt. Hell we could hire someone at $15 an hour and have them sit underneath the pole if need be.
3) Make all playoff series best of 7 (except for the wildcard). It may not be tv friendly but that's the way the game was meant to be played. I get rid of all of the off days between games to speed it up.
Those would be my three changes on Day 1.
In terms of other things, I'd try using a robo ump for balls and strikes in the pre-season. Personally I think I like how the ump blows some calls but then again I've never seen a game with a robo ump. Plus it seems like the technology could easily be manipulated to benefit certain teams so I'd like a human but I'm not opposed to trying it out in the pre-season. Plus we need jobs. Robots are killing all jobs in this country.
I'd also like to see a home plate that sits over the plate like regular base (maybe it pops up or something?). It drives me nuts that a player is out because his foot didn't hit the non-existent bag at home. It encourages them to slide headfirst which isn't safe. Either that or say that if their foot is over home, they are considered to be home.
Lastly, I"d consider saying if you beat the throw and stay and don't fall of the bag then you are safe. These permanent tags/pushes are annoying as others have said.