Cannot connect Nexus 7 to computer to see internal storage after flashing Cyanogenmod
Ran into the exact same problem: Nexus 7 wouldn't properly connect as MTP device on Windows 10 after flashing CyanogenMod 12.1. The driver I had installed was the "Universal ADB driver" (not "Android ADB Driver" as OP). It was needed during the flashing procedure.

Solution was to uninstall the ADB driver: Right-click on the device in the Device Manager and select "Uninstall". Then unplug USB cable and reconnect. Device now works as expected.