Better flowing exhaust will increase MPG's.
You are assuming the Kawasaki engineers are stupid, then. There is nothing wrong with the "flow" of the exhaust through the stock muffler. The stock muffler is designed for the best balance possible for engine performance, fuel economy, durability, and sound attenuation. They did a good job, although some people think it is too big/heavy, I think it looks just fine. And unless you are performing tons of other weight-related replacements and mods, the small amount weight doesn't matter much.
Also, it is mostly a myth that replacing a stock muffler will gain any power. A modern, fuel-injected bike is designed to run with the factory muffler, and unless you also reprogram the fuel injection system, there will be little to no additional performance. And even with, the change is still small. It only really matters if you are changing a bunch of stuff too (injectors, ports, headers, FI programming, filters, etc).
Most peoples' motivation to replace the muffler is to create more noise pollution and/or to try and impress other people.