This is how the MLS playoffs should be. Home teams listed first.
ROUND 1
East
#1 D.C. United – #2 New England
#3 Columbus – #4 New York, loser eliminated
West
#1 Seattle – #2 Los Angeles
#3 Salt Lake – #4 Dallas, loser eliminated
ROUND 2
East
D.C. United-New England loser vs. Columbus-New York winner
West
Seattle-Los Angeles loser vs. Salt Lake-Dallas winner
SEMIFINALS
East
D.C. United-New England winner vs. Round 2 winner
West
Seattle-Los Angeles winner vs. Round 2 winner
FINAL
East winner vs. West winner (or vice versa)
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It’s called the Page playoff system (or a slight variant thereof). Every seed gets a unique reward. The top two teams in each conference get a second chance if they lose their first game. The first-place team gets to host that game. The second-place team hosts the next game. The winner of their game hosts the semifinal. The third-place team hosts its first game.
Cool, isn’t it?
You could mix it up a bit if you like. Maybe the losers switch conferences so no team plays another one twice.
I’ve been pushing it for years. Not stopping now.
Duresport.com 
A couple questions to toss out there about the system:
* Do you really want that Game 1, where it ‘ought’ to be a big game because the two top seeds are playing, but it isn’t really such a big game because either team can straightforwardly survive a loss (the loser is still one victory away from the Conference Finals, and that game is at home).
Having had LA and Seattle just play twice in a row where it was relatively debatable what was at stake (witness Keane being rested in the last one), do you want them to play again, where it’s still kinda debatable what’s at stake?
* Suppose Seattle (your Shield winner) thrashes LA in that game. Then suppose LA survives the losers’ bracket to get back to Seattle in the Conference Final, whereupon holds Seattle to a 0-0 for 90 (or even 120) minutes and wins via penalties. Do we have any confidence in LA as a champion at that point?
None of those results are far-fetched or weird — in fact, on the wiki entry for the Page Playoff, all of them involve the championship match being a re-match, and being won less convincingly than the opener was (ie the champion would not have been the champion if those scores were aggregated).
The (former) Australian system, which I actually quite liked.
Puts a benefit on finishing top two, because you earn a second chance if you blow the first round matchup. (And a 1-2 matchup is much more interesting than a 1-4 or 1-8 in the first round, let’s be honest.)
It’s different from most systems we normally see. It gives date and hosting certainty for the finals and time for the host to sell it. And there’s a clear benefit to winning that first round series.
I like it. It won’t happen here, but I like it.
I think MLS only has two “good” options for the playoffs (I consider being “good” if the playoff format rewards the regular season results):
a) Single elimination games with higher seed hosting. Simple, better scheduling, less games but more at stake, therefore more fans and entertainment (less is more). See the Hyundai A-league playoffs (it seems to be working well for them). 5 teams per conference, keep the 4vs5. If a 5th seeded team wins MLS Cup, they would have beaten at least 3 teams on the road.
b) Group stage, seeds 1 and 2 host 2 games, seeds 3 and 4 only one game, followed by inter-conference semifinals and MLS Cup. It is more complicated, but still allows for better scheduling, maybe allowing to sell playoff ticket packages, and a team won’t crash in one bad game. There is the possibility of 1 game per conference group stage being meaningless.
I am pushing for option a).
My recommendation has been a 2-game (because I think that’s the number of dates the league wants to book, personally I’d be fine with single-elim) decided on points. That way we go to the 30-min OT whenever the points are tied, rather than only if the aggregate is. Higher seeds (who are the home team for that OT) have a strong tendency to win the series that get that far (9 out of the 10 that have been decided in OT have been won by the higher seed).