Actually, baseball balanced it perfectly through 1993. Divisional play began in 1969. When the leagues had two divisions a piece, you still had the importance of a table, as only the divisional champs moved on to the playoffs. There was no wild card; so it didn't matter that the teams in the American League's and the National League's Eastern divisions played a different schedule to that of the teams in the leagues' Western divisions. What mattered was that all teams within a given division played the same schedule.
Up through 1993, the division titles were prestigious championships in themselves. Just this year the Blue Jays held a celebration of the 30th anniversary of their 1985 AL East title; and the White Sox did the same a couple of years ago in honour of their 1983 AL West championships.
Since the twin abominations of the wild card and interleague play, all this has gone out the window. The wild card, introduced in 1995, brought us teams playing different schedules but competing for the same prize (the same problem with the Supporters' Shield); and interleague play, introduced in 1997, only exacerbated this problem. The prestige of the divisional title has been destroyed. In 2001, the Cardinals and Astros tied for the NL Central title. But they played no playoff game to decide the championship, as had been done in such instances up through 1993, because the loser would have been the wild card anyway.
Regarding MLS, I'd say that the optimum schedule would be one in which teams play two games against each conference opponent, and one game against each team from the other conference. Of course, this works only if you have the same number of teams in each conference, which MLS had not tended to have lately until this season, and will not have once Minnesota United come in (assuming that they come in alone, without Miami). Such a schedule would have given MLS teams a 28-game schedule for this year, and would yield a 31-game schedule in an MLS with two 11-team conferences. While this sort of schedule wouldn't solve the problem of the Supporters' Shield, it would make the conference standings more meaningful.