I'm no mechanic
but I thought that you wanted the gases to mix, as the pressure wave from one cylinder causes some back pressure at the other, effectively helping to seal the valve. From what I've read (ie don't take my word for it), the exhausts are tuned so that the back pressure hits the cylinder just as the valve is about to close, thus helping keep the fuel/air mix in place. I guess if you had two exhausts you would effectively have to tune them like two single cylinder engines. It obviously can be done, but I'm not sure I can see the benefit.
Anyhow I'm a biochemist, who reads too much and thinks he knows more than he does, so take all this with a pinch of salt.
TobyS
Oh, and I take it you don't plan on carrying luggage. Otherwise you'll have to have an underseat end can (or two) to fit the current systems? Still if you want it enough, there's bound to be a way to do it. TS