4 into 2

[Shuriken]

Fred--
I believe the advantage of the 1/3 2/4 split was for cylinder scavenging as a performance idea (which does work). Most 4-2-1 pipes connect this way as well. The stock system does not take advantage of the scavenging, but then also does not have the fat midrange problems, either. 1/2 3/4 works well to make smooth power across the entire range. With the other system, in the rpm range just before the tuned (come on the pipe)range, the sonic exhaust waves which create the big boost when the engine comes on the pipe are working at a frequency below optimum (actually moving toward the cylinder on the intake stroke) which will actually blow back through the carb. This creates a double negative for the following reasons: First, the exhaust gas passes through the carb, picking up fuel as it goes (a carb works in either direction on the venturi principle). Then, since that particular cylinder is on the intake stroke, the "fresh" air (which is already diluted with exhaust and rich in fuel) passes again through the carb, picking up fuel again. So now your intake mixture is twice fueled, and loaded with exhaust gas. This is seen as a huge rich spot on a A/F ratio, just before the big power boost usually seen around 5K rpm (and worse with an airbox). Most guys will tune this with the midrange needle to an acceptable level, or shift around the dead spot. In the "on the pipe" range, the sonic exhaust waves in the pipe are travelling out, (not in, as previously) effectively creating a vacuum in the cylinder drawing in only fresh, once fuelled mixture, and lots of it, creating the big power gain.
The 1/2 3/4 system places your exhaust strokes so far apart, that this problem is eliminated, since the exhaust strokes of the two cylinders tied together never line up with an open intake valve. It makes smooth power all the way through, though slightly less on the top end. But you will never have to deal with the dreaded "mid range bog" of the other system. It is much more rideable and tuner friendly, which is probably why Yamaha went that way in their production bikes.
Tyler

Very well said. Nice explanation.