IMO I would opt for the aftermarket radio/nav unit and save the money. You are able to get better sound and sound control with and aftermarket head unit. shop around and you will find a radio that has all the same features, but the sound quality is tops. I went with a Kenwood DNX 9960 for my SUV. For what the dealer is going to charge you for a NAV unit you can outfit the car with better aftermarket radio, amp, speakers, and sub.
On the other hand having the fatory radio/nav is also a nice feature due to the fact that you don't have to part with your vehicle while they install.
I just ordered a 2012 NISMO Z and this is the aftermarket system I was looking to purchase:
1) Kenwood DNX 9980HD $1,800.00 radio
2)Alpine PDX-5 $600.00 amp
3)Boston Acoustics SR60 $300.00 6-1/2 seperates for doors
4)Boston Acoustics S35 $60.00 3-1/2 2-way for the rear
5)Wicked CAS 370z Magic Box with sub $820.00 JL 13TW5
Total: $3,580.00 For superior sound quality and happiness.
Remember that my personal taste is high fidelity sound.... just the way I am.
-Koffeegy