If I were the new commish...
Some of these ideas were already bouncing around in my head, while others have been combined from other posts I've seen that meshed with things bouncing between my ears. My ideas will not all be popular, but that's part of the fun.
Expand the MLB to 32 teams and reorganize the league into 8 divisions of four teams each. The two additional teams would come from a place in the US where baseball pro baseball is basically out of reach. I like the idea of Billings, Montana, as some have suggested. I also like the thought of Calgary or Edmonton, Canada, but I don't think that is realistic. Instead, I would go for Salt Lake City or the SoVa/NC/TN area (Greensboro/Winston-Salem, maybe).
The DH position would be an optional position in both AL and NL, determined at the time of roster announcement (that is, before the game starts). Once announced, the team would not be allowed to change their mind during the game for any reason.
Replay would be used like it was in the LLWS. Each coach would get one challenge, and a 5th ump would be in the booth and could call for replay usage. Replays would be for home runs, fair/foul, and outs. Balls and strikes would remain with the home plate ump and/or base umps in the case of check-swings.
Pete Rose would be reinstated immediately. He would be eligible for the BBHOF as a player. Players and managers currently banned but have since passed on will automatically be reinstated upon their death and therefore eligible for HOF status.
Salary caps with penalties for abuse/overages in the way of discounted tickets/concessions and/or retribution to be spread among the other teams in the MLB. Frankly, I would have to have more info on how this would be implemented. This would probably be the biggest, most difficult item on the agenda.
I have also considered instituting a "no confidence" voting mechanism where the ticket holders (both season and single-game) could issue such a vote against the team's current ownership. Should the current owners receive 75% of the "no confidence" vote by the end of the season, the owners would then be REQUIRED to offer the team for sale for a fair market value and be required to relinquish the team should a valid buyer be found. As with salary caps, more research would be needed in the actual implementation of this aspect.
Interleague play would be phased out. I have never been a fan of it.
The regular season would last 160 games. Schedules would be arranged such that teams would play equal numbers of home and away games (I haven't done the math, but I think this is feasible with the expanded league).
The All-Star game would no longer determine home-field advantage and instead would return to an exhibition game. There would need to be an offsetting incentive for players to want to play in the game, so I would have to evaluate several scenarios in which incentives or enticements would be incorporated.
Games would be played until there is a winner. If you gotta use your shortstop as a pitcher, so be it.
Games would last nine innings at a minimum (except for weather, in which current rules apply). None of this 7-inning game-length talk. That is ridiculous. Besides, how many games ALREADY go beyond nine innings? Cutting back to 7 would not be worth messing with.