Modifications of the settings are at your own risk.
I had the same problem as the OP on my Aspire S3 laptop, and luckily, disabling xHCI mode in the BIOS was a solution for me too.
I've run all updates before upgrading to Windows 8.1. And up to this problem, I have never entered the BIOS (let alone change any setting there).
I don't understand your argument about "hardware compatibility", since we are talking about an upgrade from Windows 8 to Windows 8.1. It is clear that the Windows 8.1 upgrade is flawed, since Windows 8 did not have this problem. It turns out it is dangerous
to use on some hardware.
Everyone understands that if a non-Microsoft person says you should change BIOS settings, that Microsoft cannot vouch for that solution.
Your response really annoyed me. You criticize a working solution, but don't offer any useful solution yourself.
As long as you don't take responsibility of the flawed upgrade software, and state univocally that "Windows 8.1 is known to malfunction and break the keyboard, mouse and USB on some hardware", the advice to roll back is simply ridiculous and arrogant.
Who in their right mind is going to roll back and accept all its consequences on the "hunch" that this may solve the problem?