Solution:

I've got the PiTFT 3.5" working with Kali 2.0.1 on a Raspberry Pi 2 using the helper from Adafruit's github, not their web site. That seems to make a difference.
Here is a walk through:
http://www.whitedome.com.au/kali-pi

Pretty, isn't she?
kali-pi_01-x-tft.jpg