I agree that the current format is less likely to result in the supposed best team winning than it did years ago when less teams made the playoffs, but the current format is more exciting for fans, creates more matchups, and makes the end of the season a lot less predictable. A lot of people nowadays are not as into baseball as they used to be, but they get excited for the playoffs, especially when their team is involved, but bust it back down to four, or even two, teams, and interest would drop even lower than it already has for the nation as a whole.
As for the Cardinals 83-78 team that won it (not 83-79; they didn't have to play their rained out 162 game because they finished the season with a 1 1/2 game lead over Houston), yes, you can call them the lousiest team to ever win a World Series, but really, they were essentially the same team that won 105 and 100 games the two previous seasons, but injuries killed them in the middle of the '06 summer, which is why they stumbled to an 83-78 finish. But they got healthy in time for the playoffs, and we all saw what happened. And technically, they were better than 83-78. They were 80-69 with a week and a half to go in the season (and a 9 1/2 game lead) before they let their guard down, Houston got hot, and they almost blew the division. But once it got close, they put the foot back on the pedal, clinched the division, and then won the postseason. Not trying to hype them up as an all-time great team or anything, but just saying that they weren't as average as their 83-78 record might have indicated.