I have the same problem with Nethunter on a Oneplus One.

Android version 6.0.1 (marshmallow)
Cyanogen OS version 13.1.2 ZNH2KAS3P0-bacon
CyanogenMod API level Elderberry (5)
Kernel version 3.4.112-yesimxev-cyanogenmod-g50246f04f42-dirty root@kali #1

No connection to USB
No connection to Bluetooth

I downloaded the Nethunter version from Kali website - OnePlus One Marshmallow (ZIP)

Not being able to use the internal wifi chip (WCN3680) for monitoring/injection I needed to use an external wifi and chose the Alfa AWUS036ACH (which was confirmed to be working with a nethunter build).

Interesting detail is that updates and upgrades from kali nethunter terminal are working fine, GET to google.com or youtube.com returns the html codes, so there is connection over wlan0. From android terminal I can use ping and it works. From kali nethunter terminal, nothing.

Apache2 server doesn't start because of problems with the random and urandom.
nmap doesn't seem to work (tested the same network ip with Kali on laptop and that worked fine)

Many of the other included pentesting apps are also not working, mainly because of the wlan0, which can not monitor/inject.

I can get it that the internal wifi won't work, but if the external also doesn't work because of an old kernel not supporting usb/bluetooth, well, where does this "Oneplus One, our preferred phone" comes from?

I've been browsing for days now, trying to find info to solve this. 95% gobblygaggle.

Is there anyone out there that truly knows something to get through this? Or is it better to consider nethunter to be "good looking, Mr. Robot show off" tinker thing and move on to more reliable and professional solutions? If there are any...