I had the cans off my 900 over the winter. After doing some work I fired it up sans cans. Sounded a bit old school muscle car at idle... never revved it in that condition.
length of pipes effects exhaust gas pressures. Inequity in pressure from one cylinder to the other will change the power dynamics of the engine. have a look at this link
http://www.burnsstainless.com/TechArticles/Theory/theory.htmlThey do a way better job explaining that I could.
So from reading the burnsstainless page and taking what you are saying, the problems is not just that the pipe is short, but that it is short and open. Short baffled, or at least choked down inside diameter of the pipe will build the backpressure that is needed.