Thus far, MLG has done three arenas. Winter Arena and Spring Arena 2 were nearly identical. Both used 32 players, both used the same, standard double elimination bracket (well, almost standard -- it wouldn't be an MLG without extended series). The only difference was how the first round pairings were set: Winter Arena went directly by seeding while Spring Arena 2 let the top half seeds draft their opponents from the bottom half. Spring Arena 1 used a much different format and only had eight players, however it seems that MLG will not continue hosting this sort of event.
Summer Arena adds another subtle change. Rather than using a standard double elimination bracket, the players will first be separated into two groups. From there, double elimination play will yield two finalists. Those two players will face off in a single championship match.
While far from ideal, I think this is a wonderful change for MLG. A key problem with using double elimination brackets is the monumental advantage held by players who have not yet lost. As the tournament should be growing more exciting near the conclusion of the event, matches taking place in the losers bracket are between players highly unlikely to ultimately win the tournament. The finals, which should be the climax, often seems predetermined since not only does one player have a large handicap, oftentimes the match is a repeat of a pairing from one or two rounds prior.
In other words, tournament does not end with a "bang". It fizzles. The winners bracket finals and semifinals are often the most significant matches. While using double elimination affords the losers of these bouts a second chance they wouldn't get in a typical knockout tournament, the losers bracket tends to play out as though they were glorified consolation matches.
Winning from the losers bracket, of course, is not impossible. But "not impossible" doesn't make an event exciting to watch. The fact is, the winners bracket player will win an awful lot, and enough tournaments have happened on the Starcraft 2 circuit for this to become apparent. For me, it actually feels worse when the handicapped player is able to put up a strong fight, but still loses (see Squirtle vs. aLive at IPL4) -- it breaks my heart to know that they could have won if the match started out on even footing.
Considering this, MLG's structure change is a good move. While last few matches before the championship will suffer the same fate as before, the integrity of the finals is preserved since two players (who will have yet to play each other) will meet on an even playing field. No advantages, no obvious result. This should make watching the finals much more entertaining.