If you had done that, the Marlins wouldn't have been World Champs and the magic of the Yanks-Red Sox in the ALCS would never have happened.
Maybe for the purists, but I think most people like it the way it is and don't want to change a thing. Fans like watching the big rivalries in the interleague games and love the buzz of things like the Red Sox coming to play the Giants and the Dodgers and Yankees squaring off. And they like the chances of the divisional rivals both getting a chance to make the playoffs when they are both having a superb year. The final straw was the Giants team that won 103 games and yet stayed home. Just think about that team, the regular season meant nothing because they happened to be in a division with the team with the best record in baseball, which promptly went out and lost.