TLDR; One must read the MEDIA module in NCSExpert and then check a setting in there and change it if needed.
I'm a very knowledgeable MINIac (or would like to think I am, ha) and it doesn't hurt being a pretty huge geek too. My MINI was ordered with all of the cool tech gadgets you could get at the time in 2013. Apple Carplay or Android Auto did not exist or even in the works yet. MINI caters to the Apple crowd more in that it literally only supports iOS older MINI Connected systems (2014 and the F56 models support both iOS and Android).
For work and in life, I'm a mobile phone guy so I had an iPhone 4S at the time and decided to go all out and get the arm rest for my MINI and the dock for my iPhone in the armrest (charges it, lets you play music from it to MINI and also play VIDEOS too!).
Fast forward to Apple's release of the iPhone 5 and the new lightning cable/port. Us MINI Connected owners were basically screwed if we upgraded to a newer phone. Armest docks were not available and I don't believe still are officially. MINI Connected itself has gone through several major revamps and most of the recent ones have not been good ones. The removal of Send to Car and the latest total redo of the app removing Dynamic Music, Mission Control and several other features has many owners upset.
However, I've come to grips with this. The new app is a bit more fluid, simple and to the point. I've also added a very nice ProClip mount for my iPhone 6 Plus ( http://www.proclipusa.com/mobile-device-holders/magnetic-universal-phone-holders/magnetic-car-mounts.aspx ) and realized I wanted to be able to use it now as my main MINI Connected / Calendar / Contacts phone.
Ok, let's just get to it. The problem I had was when I plugged in my iPhone 6 Plus via the official apple sync cable into my MINI NO SOUND would be heard through my speakers or the system. My iPhone would show the songs and album art but ZERO audio. I can use the MINI Connected app just fine with it so I figured it was time to start digging deep into the code via NCSExpert.
TLDR; One must read the MEDIA module in NCSExpert and then check a setting in there and change it if needed. Default is analog but we want to change to digital so we can use our iPhone lightning cable.
Mine was set to analog and once i changed this my iPhone 6 Plus and Apple cable let me start listening to music via the front usb. So this now makes me wonder if you even need a new Y cable for full MINI Connected features. I will test video playback but as a backup use my iPhone 4S i have in the armrest dock for that needs (i have about 240 music videos of my fave songs on there i play in traffic).
USB2_IPOD_AUDIO must be set to analog if you have an older iPhone in the armrest dock; however if you have a newer lightning dock, you may have to change this setting to digital too. i did verify that changing to digital w/my iPhone 4S muted all audio from it.
Hope that helps some other MINI Connected user!