I'm not knowledgeable but I can only recall one SoC providing usb3.0, mind you those things are for embedded/phone devices, thus usb3 looks like a costly overkill. I'm all for it but that's hardly a motivation for them.
usb2 would be fine if it was a sane implementation but AFAIK the rpi SoC was made for ~video-only appliances where there's close to no IO or cpu processing and thus the usb stack firmware code do some bold decisions that induce a nice penalty on usb/cpu.
It's possible that they released a new version since (my data dates from a few monthes ago) or that someone published a binary patch to improve the situation.
I think USB 3 is prohibitively expensive at the moment. Power may be an issue there too - you barely get 200mW out of the USB ports by the time the system itself is powered.