I like the idea of doing away with the NL and AL. I know the purists shudder at the idea, but going with a totally geographic divisional allignment would create some incredible new rivalries (NYM-NYY, NYM-BOS, PHI-NYY, WAS-BAL, LAD-LAA, OAK-SFG, KC-STL, CWS-CC, CIN-CLE and on and on...).
I like the idea of five 6 team divisions (play 18 games vs your 5 division foes for 90 games and 3 games vs everyone else for 72 games- 3 x 24 teams).
You get 3 wild card teams with no play-in needed. Seed the playoffs by best record with division winners getting no special preferences for winning a division with an 84-78 record.