I'm in the totally stock exhaust, carbs, intake, etc. camp, and I plan to stay that way. Sure it's a lot of grief to remove and replace, but that shouldn't be necessary as long as I care for the bike properly. Some people enjoy the challenge of modifying exhaust, rejetting, etc. Personally, I don't get much out of it. I enjoy the power and efficiency of the stock bike. Is it possible to get more performance out of the bike? Sure, probably, but I'm pretty skeptical that there is a measurable increase. I think it's probably more likely to be a decrease in many cases.
Years ago I had an '81 Yamaha XS650. I laid it down and rashed the exhaust pretty badly. Ended up buying the bike back from the insurance company and replaced the stock exhaust w/ a 2 into 1 Mac system. The bike never ran properly after that despite re-jetting numerous times. Yeah, I know different bike, different issues, etc.
Also had a '97 Suzuki Intruder for a couple of years. Owner had swapped out the stock exhaust for a Cobra system, but never bothered rejetting the carbs. Bike ran way lean, and turned the oil black in a very short period. Was also loud and obnoxious to my ears. It was fun at first but got old fast. I was able to re-jet and get it to run acceptably, but was way more trouble than it was worth (to me!).
I learned from those experiences that this aspect of ownership is just not my thing. . . . It's a free country, though. Everyone needs to decide what they want to do with their bike!