I have just gone through very extensive tests with USB3 external drives and my mid 2012 Macbook Pro (non Retina).
The short answer is that if your Mac has USB3 hardware, you can read and write via USB3 when booted into Mac OS, and take advantage of its greater speed. (Some people have reported that you may be stuck at USB2 speed if the first device connected to the port is USB2. But you can always fix that by just rebooting.)
HOWEVER the boot ROM of many of those Macs does NOT support USB3. To boot from a clone you have made on a USB3 drive, you need to connect your drive via a USB2 hub or USB2 cable. It will operate at USB2 speed but it will work. Interestingly enough, the clone may actually appear to work better on older Macs that do not support USB3 at all, because of course the drive then operates in USB2 mode.
I have submitted a bug report to Apple, but there is no guarantee that they will choose to develop updated boot ROMs that support USB3 for older Macs with USB3 ports.
As others have said, you have to use Disk Utility to partition in GUID format, and format the drive as Mac OS Extended (journalled) to have a bootable drive. But that's easy. And you can even choose to encrypt the external drive. As long as it is connected via USB2 at boot time, it boots just fine once you unlock it with your password.