USB3 should be bootable as well as thunderbolt.
DON'T rely on a USB flash drive to store anything that's important to you.
DO get either a USB3 or USB3.1 gen2 drive. Gen2 is faster, but will run warmer.
BE AWARE that if you rely on an external drive for storage, that you ALSO must back that external drive up, as well as backing up your internal drive.
So... when you come down to it, you need TWO drives (primary external and external backup).
My opinion is... might be just as cost-effective to "pay Apple's price" for the extra internal storage...