Well you also have to keep in mind that season W-L records are an imperfect statistic in the measure the quality of teams due to the vagaries of scheduling, the relative strengths of divisions, and injuries throughout the season. A "second place" team can have a better record than all but one team (or theoretically end up tied for first) in each league -- refusing that team a spot in the playoffs perpetuates an inequality of a different kind...
Ultimately though, this "seeding mentality", common in college basketball and professional football and professional basketball, which maintains that the best record must have the biggest advantage (via buy weeks or seeding) is pretty much rendered moot by the size of the baseball playoffs. Only four teams from each league. Thats half the size of the NBA, 2/3rds the NFL and 1/17 the size of the NCAA. The proverbial wheat has already been separated from the chaffe. Any of those four teams can beat any other -- which is proven often enough by the playoff success of the wildcard. The top four teams get to PROVE who is the best team on the field.
Take the NL 4th place (wildcard) STL Cardinals for example. They beat Philadelphia (best record in baseball), Milwaukee (tie 3rd best in baseball), and the Rangers (tie-3rd) to win the Championship. Thats why we play the games folks. Are you really going to say they had an unfair advantage because they didn't win the division...never mind the fact that Pujols, Holliday, Freese missed significant time during the season...never mind the fact that the Cardinals had a winning record DURING THE SEASON against each of the division winners (Phi 6-3, Ari 4-3, Mil 9-9).
Is the baseball season too long? Probably. Will punishing Wild Card teams do anything to improve the quality of baseball in the playoffs? No. Instead baseball is actually diluting the game by adding another team and provoking a farcical 1-game playoff. Thats definitely NOT how to ensure the best teams move on. That, along with the idea an exhibition game (All Star) determines which league gets home field, and the miserable handling of the Ryan Braun steroids case are reasons why Bud Selig is bad for the game of baseball.