Well you have a very valid point, but you need to look at all sides of the puzzle. Although performance is pretty important, it's not the #1 reason to design a product.
Reliability is very important also. Sure, maybe the stock exhaust system doesnt produce the maximum amount of horsepower, but it keeps the noise down (EPA), and maintains it's basic look years after purchased. It may not work the best when looking for horsepower gains, but when you consider durability and and noise control, it works pretty well.
The key word is balance. Remember how much of a wheelie monster the 1997 TL1000s was? I had the pleasure of riding one of these motorcycles, picture a busa with about 240 horsepower and no timing retard in gears 1 through 3, thats what this bike felt like. This bike was sick. You could flip that bike in any gear with a little too much throttle, and guess what?
No one wanted it, scared the sh*t out of people
Balance is everything. Manufacturers have to consider things such as durability, comfort, reliability, control, and horsepower.
For every 1 busa owner with 500hp in his bike, you have probably 5,000 who left the bike pretty much stock, and are happy with it that way.
Bolt this on here, port this, change that, disconnect this, plug in that, add this, tweak that, shave a little here, remove that. Thats the fun part! Do you want the manufacturers to do this for you?
Mike