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With 5 or 6 teams, there's no way around it :- )
5 teams -- the 2 WC's play each other, and then you're down to 4 teams ....
6 teams -- the two best records get byes, the "worst" division winner plays the first round with the three WC's, and then you have 4 teams again.
So, it would actually promote the #1 regular-season team winning more often than it does now.
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That's a great point, that in baseball, the inferior team has an inherently better chance than it does in the NBA and NFL. BABIP and Pascal's Triangle weigh heavily ('it's a game of inches").