Looking at the comments on the article
The Ultimate Storage Solution? inspired me to do some research into USB3. I was guessing that most of the speed loss (5Gb/s =<bits to byte>> 625MB/s =<8/10 encoding>> 500MB/s) from 500MB/s was due to the device being slow (flash/or the disk controller) but apperently there is issues with the protocol itself.
This article (i do like tomshardware, he has done many good reviews int he past) explains more problems with the protocol. Apparently the USB3 protocol stats that 400MB/s is realistic after more overhead (flow control, link status, framing,...). Then also the data communication protocol (BOT Bulk-only transport). This doesn't allow for command queuing, (think assembly line). There is a new replacement for BOT but it's not widely implements (including no drivers in windows 7) called UAS.
Faster USB 3.0 Performance: Examining UASP And Turbo Mode : USB 3.0: Dude, Where's My Speed?
Anyways i thought it was a good read.