by support »
Hello,
Wanting something hotpluggable sounds like a good reason to go for USB (PCIe is in theory, but that feature doesn't seem to have taken off).
As for the data rate, 5 Gb/s corresponds to a Gen2 PCIe lane, which typically gives 400 MB/s. So don't expect any dramatic improvements. I can't tell what the actual figures will be as of now.
There's also an inherent difference due to the nature of the physical link: The wiring for a PCIe link is short and controlled, while USB is, well some cable and a couple of connectors. Bit errors on the link are extremely rare on PCIe, but I won't be surprised if there will such issues with USB 3.0. There are retransmit and recovery mechanisms in the protocol, however these disrupt the data link momentarily. Might not be a big deal, but can be at high data rates (the FIFO's FPGAs may overflow, for example).
At the moment, these are open-ended speculations. More hands-on experience to be gained later this year.
Regards,
Eli