On one hand, I really want WebUSB, but at the same time, I REALLY don't want the average person to have WebUSB.
Practice has shown that consent popups do not work and people will manage to give consent to anything without even realizing it ("I never clicked on anything", they say, while I swipe away 50 spam push notifications and remove push permissions from about a dozen "news" sites).
Honestly, I kind of like the Internet Explorer version of permissions, where you needed to mark certain sites as "trusted" to enable certain features. The process is hard to discover, takes a decent amount of time, is a bit confusing, done in a system-styled modal popup with reasonably scary and large warning icons.
If people had to go through this process to mark a site as "trusted" in order to use WebUSB, WebBluetooth, and the other dangerous APIs, far fewer would do it by accident. The UX would still be better than installing a native app and you get sandoxing as a bonus, so I think the tradeoff would be worth it.