Usually engineers have sweated out most of the details. The air box and exhaust and the engine work together to provide you the best compromise of performance, fuel economy, vehicle cost and emissions. They've measured the optimal lengths and turns to produce a supercharging effect at engine speeds you will most likely spend time in. If you start replacing components on your own, you're throwing out the work of the engineers right out the window.
Say for instance you did get an aftermarket exhaust. Then you'd hope the fuel computer can adapt so it doesn't run lean with annoying (or cool) backfires, and that the additional fueling makes up for potential loss of low or mid-range torque. If it doesn't, then you may need to figure out how to increase the fuel to the injectors. Once sorted out, it might work great on a race bike that gets the beans revved out of it. Will it work for your usage scenario?
Plus, with a loud exhaust you might just annoy your friends who ride behind you. I usually pack ear plugs for scooter and motorcycle rallies. It's no fun being that guy that people talk poorly about.
Or say you get a drop-in reusable filter or perhaps axe the air box completely and put one of those fancy cone filters. Is the filtration efficiency (read: not flow rate, but rather how much dirt can it capture) on par with the stock dry paper filter? What happens if you hit a puddle or encounter rain with the latter? I've had people pull over on rides to empty out their wet carburetors. Will it start and idle well? The stock intake is meant to increase turbulence and promote even mixing of air and fuel.
After those mods, you'll need to figure out what your new power band looks like and how to set up your CVT to stay in the sweet spot. Roller weights, contra springs and test runs. Better get an accurate tachometer; otherwise you will be fumbling in the dark.
Personally, I suggest a faster bike if the time comes where you need more oomph. Someone else isn't likely to pay you for the effort you've spent on souping up your bike.
Still, you may enjoy the allure of putting your personal touch on a bike.
