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Ya, I mean how often does the #8 or #9 team win in NBA or NFL? Never. Happens all the time in baseball, and now we'd be talking the #10 or #12 teams..
I like the "bye" format though. It doesn't really change the current format of the playoffs, but it gives more teams a crack at it. Now you have some incentive to create a great team in the regular season and its even more epic if a bottom team defies the odds.