Carried to its logical conclusion, that argument leads us back to pre-1969, a time when ONLY the best team in each league gained admittance to the World Series. I'm sure you'd have been saying exactly the same thing in 1973 about that dadgum division setup that allowed the far-superior Reds to be bumped off by the mediocre Mets. And from a purist level you're exactly right about all of it.
Alas, there aren't enough purists to go around. Most fans care about their local team's fortunes far more than they care about the sanctity of the World Series. The same system that used to maximize the potential for a memorable Series ensured that all but a few cities had rolled up the sidewalks to the ballpark before Labor Day most years.
And then there's the pragmatic current-day Reds fan view: how likely is it we're going to be THE best team in the NL this year? If that's what it took, the anticipation level around here wouldn't be nearly as high, in my opinion.