Here's my crack at alignment:
NL East: Mets, Braves, Marlins, Nats/Expos
NL Central: Cubs, Cardinals, Pirates, Brewers
NL West: Padres, Dodgers, Astros, Reds
AL East: Yankees, Red Sox, Orioles, Blue Jays
AL Central: Tigers, Indians, Twins, Rays
AL West: Royals, Mariners, A's, Rangers
Rationale: The Astros spent a long time in the old NL West, as did the Reds. The Rays are the farthest west of the AL East teams. The Royals are the farthest west of the AL Central teams, and also have a lot of history in the old AL West. Kind of a mix...more history in the NL, more geography in the AL.