A few things I would do (some are similar to RJM's ideas, some aren't).
1. I don't like the idea of another wild card team. In fact, in many cases the wild card team is the second best team from a league (for example, right now the two best teams in the AL are NYY and TB, but TB would be a wild card). I would consider doing away with divisions and just take the four best records in each league. If the season ended today, the Red Sox would miss the playoffs despite having a better record than the AL Central leading White Sox. If anything, in order to punish the #4 team and reward the #1 team, then in the first round, the #1 team gets the first and last two games of the five game series at home.
2. Doing away with divisions would lead to my next change, which is sending an NL team back to the AL. The most obviously candidate would seem to be the Brewers, since they were most recently in the AL anyway. Sure, this would mean that there would always be at least one interleague series going on, but....
3. I would make both leagues use the DH. I don't need to see pitchers hit. If they happen to come up with runners on base, then they bunt. Yippie! If not, they look totally clueless in most cases and seek the quickest u-turn possible. Pitchers hitting really don't add any intrigue and/or sophistication to the NL. Let's be honest, the double switch isn't all that complicated. Besides, this would allow pitchers to go deeper into games because you don't have to hit for the pitcher in the 6th inning. And double switches are even worse because not only are you removing your best pitcher, but you're also removing one of your starting position players. Now the fans, who want to see the best players, get to watch a middle reliever and a fourth outfielder. Awesome.
4. I would at least consider contracting two teams. The Marlins would be the easiest target. I'd let the state of Florida have one team and they could do whatever they wanted to with that team. They would have the rights to all of Florida, plus Puerto Rico, so they could play some games in Miami, some in Tampa, some in Orlando, and a few in San Juan. I'm not sure who would be next, but if I went this direction I think you could get rid of the worst 50 players in the league, which would improve the quality of baseball.
5. I would shorten the season to 150 games and consider doubleheaders once a month (April through August). That would slice 17 dates off the schedule. Of those 17 dates, I would add 7 off days during the year, and shorten the season by ten days so we're not playing the World Series on Halloween or in October. Yeah, I know the owners aren't going to give up dates because of the ticket revenue, but I'm making these changes in a perfect world.
6. I'm in agreement regarding Joe Morgan, Tim McTalksalot, and Joe Buck.
I also agree with zombywoof, no need for the MLB champ to play the Japanese champ.