Thanks for the update.
First the good news: I just verified that I too can now boot my mid-2012 Macbook Pro from an encrypted clone of my boot drive (made with Super Duper!) using a USB3 drive with no intermediate USB2 hub. So with El Capitan Apple has eliminated that annoying glitch.
Now the bad news. It boots really slowly. In fact I see no significant difference in boot speed whether I connect the USB3 drive directly or through a USB2 hub. So I am pretty sure that Apple took the easy way out and chose to boot USB3 drives in USB2 mode. And the drive seems to be running at USB2 speed even after I log in, when OS X certainly has full USB3 support available.
Of course it could be that my USB3 drive is just a slow drive and it is the drive not the Mac that is limiting performance. It's a "slim" Seagate 2TB portable, so I don't expect it to be a speed demon. I will try some tests and see what I find. For its main purpose of backup, speed is less important than reliability plus small form factor that will let me carry it everywhere. I'm using .5 TB for a clone, and 1.5 TB for Time Machine.