The most common mod to stock exhaust is to drill around the baffles. I think some guys have even removed the baffles. Like you, I wasn't as fond of the aftermarket exhausts available for this bike, I feel like Yamaha did a great job aesthetically with the mufflers. However, I couldn't stand the lack of aggressiveness enough that I changed it out for a slip-on. I talked to a couple of places about modding the factory exhaust, but no one wanted to mess with it (after removing and inspecting the stock muffler setup, I could see why).
Good luck with your bike, I hope you find someone to make it the way you like it.
Good luck with your bike, I hope you find someone to make it the way you like it.