I installed 4000nex last month and tried different hookup and settings. 

This is what i have ended up with and everything works as expected.

iPhone 5s is mounted on dash mount with apple av adapter mounted in the dash mount. the hdmi cable is ran to the head unit, the usb to lightning cable is run to charger, not usb1(note: pioneer instructs to install this to usb1, but it is for charging only, not for reading iPhone, the apple av adapter has two slots 1. hdmi 2. lightning. The lightning slot is only wired to the charging part of the iPhone, while the hdmi is wired to the audio video part of the iPhone, hence the incompatible usb error message)

Appradio uses bluetooth and hdmi for connectivity, not usb1. I have thumbnail with pics on usb1, 80gb ssd on usb2 and 32gb sd card in sd slot. I have full function App Radio, AHA, Pandora, bluetooth phone, etc.

I purchased obd2 wifi unit for Dash Command app, and have access to all my engine functions, with ability to read and clear codes. I have 11' headrest screens for rear viewing and the ability for wireless headphones for rear passengers, if they want to watch a movie while i listen to my music library. The dual zone works great. 

Nice

What functions would be available if you attached the iPhone to USB (without hdmi)? This is what hasn't been clear to me. What do you gain/lose by going between just USB and Bluetooth, versus hdmi and Bluetooth (obviously this gets you appradio).

Music playback. Pandora. Aha. Those all work with the 1-wire setup. 

You don't get video or anything like that.

What functions would be available if you attached the iPhone to USB (without hdmi)? This is what hasn't been clear to me. What do you gain/lose by going between just USB and Bluetooth, versus hdmi and Bluetooth (obviously this gets you appradio).

Just like kokenka said, pandora, aha, however You also get iPod function from the iPhone if you select USB as your smartphone connection and charging.

If you do not ever plan on using app radio, there is no need for apple av adapter. If you have av adapter hooked up and choose hdmi as the input, you basically mirror the iPhone, the picture is small, and there is no touchscreen functions on the head unit. it only mirrors the iPhone screen. When using only the lightning  to usb, you will get  everything except app radio. just be sure and hook up to usb1.

When using only the lightning  to usb, you will get  everything except app radio. just be sure and hook up to usb1.

You will not get video.

So USB only you get pandora, aha, and iPod functions. Can't you do all of those if you have appradio mode setup though? I'm just wondering why you would ever do just USB unless you were absolutely never going to do appradio or mirroring?

app radio is horrible. I dont ever see myself using it. I dont use pandora or Aha. Ill stick to the usb cable. Ill wait and see how car play is for the radio