The biggest contributor to the problem, imo, is the divisional setup, which drives the seeding. Get rid of divisions, top 4 teams from each league make the post season, two 7-game series to make the WS. 162 games without divisions will yield seedings that are a better reflection of the quality of the teams (without as many divisional game I think that Phillies would have finished ahead of the Brewers and Jays ahead of the Rangers, for example).
Geographic divisions are meaningless with modern scheduling, so it's kind of bullshit that teams like the Rays and Phillies need to essentially play their way into the divisional series when they played in objectively tougher divisions than the AL West, for example, and had a better record in the case of the Rays.