Having a separate partition for /usr is not a problem for VirtualBox user, mostly. Normally, by installing Oracle VM VirtualBox Extension Pack, USB 2.0 feature will be usable. But with separate partition for /usr, udev will not be able to run a shell script (/usr/share/virtualbox/VBoxCreateUSBNode.sh) since /usr needs to be mounted first. This shell script creates /dev/vboxusb and its content which are needed to use USB 2.0 feature in VirtualBox. Without executing this shell script, the USB devices menu is disabled.
Relevant system specification:
Acer Aspire 4741
Debian GNU/Linux Wheezy (testing) as of 2011-08-12
VirtualBox 4.1.0
udev 172