The same problem here. Upgraded from 13.04 to 13.10, kernel 3.11.0-13 and USB 
3.0 is not detected.
lsusb output:
`Bus 002 Device 004: ID 0955:7002 NVidia Corp. 
Bus 002 Device 003: ID 093a:2510 Pixart Imaging, Inc. Optical Mouse
Bus 002 Device 002: ID 8087:0024 Intel Corp. Integrated Rate Matching Hub
Bus 002 Device 001: ID 1d6b:0002 Linux Foundation 2.0 root hub
Bus 001 Device 005: ID 0bda:0139 Realtek Semiconductor Corp. RTS5139 Card 
Reader Controller
Bus 001 Device 004: ID 04f2:b1bb Chicony Electronics Co., Ltd 
Bus 001 Device 003: ID 0cf3:3005 Atheros Communications, Inc. AR3011 Bluetooth
Bus 001 Device 002: ID 8087:0024 Intel Corp. Integrated Rate Matching Hub
Bus 001 Device 001: ID 1d6b:0002 Linux Foundation 2.0 root hub`

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https://bugs.launchpad.net/bugs/1242321

Title:
  USB 3.0 not recognised by Ubuntu 13.10

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