The NCAA identifies its tourney brackets by geographic region. I will instead use the first names of the four Beatles. (It does tie into 1969, at least).
The John, Paul and George brackets will contain the 1969 and 2009 teams. The Ringo bracket will have the 1987 teams.
I am "seeding" the first three brackets, in effect, in the second round. The first round will be strictly paring the franchises 1969 and 2009 teams: The 1969 Yankees vs. the 2009 Yankees, the '69 White Sox vs. the '09 White Sox, the '69 Seattle Pilots vs. the 2009 Milwaukee Brewers, and so forth.
To get the seedings, I added up the regular season wins for each pair, then created eight groups of three and filled out the brackets accordingly. When two franchises tied, the higher seed went to the the best single-season record. (There were three such cases.)
1st seeds: Twins (184 wins), Yankees (183), Red Sox (182)
2nd seeds: Dodgers (180), Braves (179), Cardinals (178)
3rd seeds: Giants (178), Tigers (176), Cubs (175)
4th seeds: Orioles (173), Senators-Rangers (173), Mets (170)
5th seeds: Angels (168), Reds (167), A's (163)
6th seeds: Phillies (156), Astros (155), Pirates (150)
7th seeds: White Sox (147), Pilots-Brewers (144), Royals (134)
8th seeds: Padres (127), Indians (127), Expos-Nationals (111)
Note that 15 of the 24 pairs were above .500 (162).
The 1969 Twins won 97 games, the '09 Twins won 87 -- 184. The Yankees were 80 and 103, the Red Sox 87 and 95.
The Cardinals were put a line above the Giants by one game: 91 wins in 2009, one more than the Jints had in 1969. The other ties (Orioles vs. Sen.-Rang. and Padres vs. Indians) were within the group.
There were no 100-win teams in 1987. There were two in 1969 and one in 2009, and it so happened that they are all in different brackets. That wasn't intentional, but it's nice that it worked out that way.