*Solved* (well at least for me)
I know this is an old thread but just wanted to post this in case someone comes across it as this issue had bedeviled me for years!
I have a 2013 MBP 15" Retina and had the exact same issue that the OP was experiencing. I tried just about everything mentioned in this thread except for the USB 2 powered hub. I was using the OWC Thunderbolt 2 Hub for my peripherals but my iLok would not work on it.
But now OWC has come out with the Thunderbolt 3 Hub so I grabbed one and a couple of Apple Thunderbolt 3 to 2 adapters, wired everything up, plugged the iLok into the hub and lo-and-behold, it "finally" works for me!!
No more eating up a USB port on my laptop just to run my iLok!!
OWC link is here...
https://www.owcdigital.com/products/...3-dock-14-port