There have been a slew of changes to USB in El Capitan that have affected a lot of people in different ways.
If a USB 3 device is slow, make sure it's connected to XHCI instead of EHCI somehow; browsing the device tree in ioregistryexplorer (or if you're a ninja just use `ioreg`) and/or seeing what System Information says (240Mbps/5Gbps) for the link can sometimes show a problem. I am more familiar with this issue manifesting on Hacs but I've seen some Apple Discussions with Mac users reporting weird USB 3 behavior or issues.
My tl;dr assessment is that Apple started defining the hardware differently (arguably more correctly according to people that apparently know AHCI/DSDT a lot better than I do) and there are some changes in behavior that should have been better across the board for Mac users but isn't always the case. On the Hac(k)intosh side this has often manifested with EHCI bus issues (and people having to re-name their EHCI devices to work around it) with most electing to route all USB to XHCI and let it sort it out. This is usually OK, but I've had instances where a USB 3 device in a hub is fine and functional at USB 3 SuperSpeed but after a reboot is only seen as High Speed USB 2 in the same port -- it's also causing many users to hit a limit on the number of USB devices that can be attached.