Arguments resting on the Western Conference being stronger than the Eastern Conference just don't make sense at all. This phenomenon is cyclical, and will even out over time. More fundamentally, if you are going to ask "why should teams from one conference be denied if they are better than teams of the other conference?", that is an argument for a single table. MLS will always have conferences; so we have to accept this inherent feature.
Furthermore, without a balanced schedule, there is no way to say, based solely on the records, that a team from one conference is better than a team from the other, because the teams in question will have played vastly different schedules.
Let us realise that here are two problems with the MLS playoffs:
1) with greater than half the league qualifying, a losing team is very likely to make it every year
2) the two-legged ties reduce the advantage of the higher seed.
Factor no. 1 would be less of a problem if not for factor no. 2. If there were no two-legged ties, then the top seeds would play at home, and the lower seeds would play on the road, thereby creating significant differences between the finishing places.
But, as it stands, there is no real difference in the finishing places; so a team that is in the playoff group has no reason to strive for finishing, let's say, third as opposed to fifth.
And if the no.1 seed got a bye, as would happen if three teams from each conference made the playoffs, then that spot would be highly prized indeed.
(You could do a version of this with six teams: #1 and #2 get byes in the first round; #3 hosts #6, #4 hosts #5; higher remaining seed plays at #2; lower remaining seed plays at #1.)
Playoffs in themselves are not necessarily bad; but, if you are going to have playoffs, then they ought not to rob meaning from the regular season. MLS playoffs use two-legged ties only to give each playoff team a home game, despite the fact that this format devalues the whole competition.
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