The Wii U Pro Controller connects using the same procedure as a regular Wiimote, except it has no option for "temporary" syncing (the 1+2 method). Authentication/pairing is still optional, the controller can work without it but it must be performed at least once (and the created link key retained) to enable "one-touch" reconnection.
Note that the Wii U Pro Controller does not have the 0x1700 bytes of accessible EEPROM memory normally found in wiimotes, any attempt to read from this area will cause the controller to disconnect. The mapped extension register area (0xA40000) can be accessed as normal, the other register areas are unknown.
Information gathered from linux "hcitool info"
Device Name: Nintendo RVL-CNT-01-UC
LMP Version: 2.0 (0x3) LMP Subversion: 0x1d8d
Manufacturer: Cambridge Silicone Radio (10)
Features: 0xbc 0x02 0x04 0x38 0x08 0x00 0x00 0x00