For what it's worth, on my Explorer 16, with a PIC32MX360F512L mpu:
It accepts the hex file (different one of course) from my Pickit2.
I can get a command line interface with my serial port (this chip does not have usb on it).
When I try to connect command line interface with my PicKit2, I get almost no response. I do get a square box at some baud rates, but that is about it.

Not a very good test, since there are a lot of differences, but it might be better to stick with USB for now.