If the league wants to have three playoff rounds (and the revenue home & home series bring), then you have to accept the fact/risk that top seeds can be eliminated easily. I would argue that a home/home series reduces the risk of a top seed being eliminated on a freak goal/call. However, it doesn't eliminate it. If the top seeds are still the best team at the end of the year, they will win. If not, it can be argued that they shouldn't win.
I understand the objections of some fans when lower seeds meet for the cup... it does seem to 'taint' the process, at least in theory, if the best teams over the course of the season don't make the final. However, that's the nature of playoff systems in every sport. I can't argue with a New England/Houston final this year. Chivas was unlucky not to beat KC (and what a semifinal that would have set up!), but that's the way it goes. DCU might have seemed a lock at the end of the season, but they didn't play well enough against Chicago... I was really surprised that the Fire didn't beat the Revs given the way they had been playing, but as the saying goes, "That's why you play the games".
I agree with the posters who have said the qualification system isn't fair. Unless the teams play a balanced schedule, you can't use overall points to determine playoff qualification (but MLS is a long way from the only league that does this, of course... in fact all the major leagues do exactly the same thing). When the league reaches 16 teams, I'm assuming either a balanced sked will be adopted or the playoffs will be locked at four east/four west. That would be my hope anyway... I've been disappointed before, of course...
MLS has chosen a playoff system rather than a season long single knockout cup (as some Euro leagues do). This is a North American preference (nearly all other leagues in NA do this). Hockey and Basketball also experience this type of criticism for largely the same reasons. Was baseball better when only the division winners advanced to the playoffs? As a purist, I think so, but most fans do not agree with me... ratings are higher now than ever before, and MLB revenues have soared since the wildcard system was introduced (my chagrin notwithstanding).
Under any playoff system, if your team is truly the best, they will come through. It's always disappointing when your team doesn't play well in the playoffs (whether due to injury or ??), but that is the nature of playoffs. It matters not if MLS adopted an FA cup style competition... There's no guarantee that the two best teams meet in an FA cup either. Injuries can result in an early round FA cup exit just as easily as the MLS playoffs do. No system is perfect.