Some ancient versions of PICKIT3 firmware only work with the also ancient MPLAB IDE (not MPLAB X).
You can download the older software packages from http://www.microchip.com/pagehandler/en_us/devtools/mplabxc/ and go to "Downloads Archive" tab.
On the bottom of the page you also have the "Stand Alone Programmer App v1.0" and "Programmer App v3.10".
Told you so O0
But actually didn't expect it to have such a major difference.
Nevertheless I agree with your video Dave. If you review the original rant video not much has changed. Yes there is an IPE, but no command-line programmer tool. Almost all other vendors have them.. (either OSS or closed) which is useful for an automated QA procedure. I can only recall a pk2cmd Linux tool and a Pic32prog tool (only PIC32s obviously), but that means you miss out once you want to batch QA boards with a PIC24E.
MPLAB X is OK; I don't really like Java IDEs and especially dont like the bugs I have encountered with Netbeans (e.g. horrible code highlighting updating or constant 1 thread 100% load while editing), but in general it makes more sense to use. I also like that it's multi-platform. It leaves me free to switch from Windows to Mac to Ubuntu, which I already did.
I share the general experience with hardware debuggers. Other vendors have their problems too:
AVR - you can brick a device with 1 wrong fuse setting or 1 ISP clock setting (thus corrupting fuses). No way to recover it back unless you connect a dozen wires for HV Programming.
TI launchpad debugger - as mentioned earlier in this thread, this debugger was very buggy when connected through a hub. The overflow of traffic makes sense.
Olimex ARM JTAG with Jlink protocol clone for IAR - it worked.. but after closing a debug session you had to reenumerate the device in order for it to work again. It was a great programmer for the cost at the time.
I can't really see a generic solution, other than to buy the more expensive hardware versions. I read that J-Link EDU is not getting as much love anymore for the Cortex m7 chips, and obviously is not to be used for commercial products. OTOH paying 300$+ for a ICD3, ULINK or proper JLINK is not great. I can see why the STM32 discovery boards are popular. They basically give away the hardware for debugging + a neat board for testing some basic code. In my experience STLinkv2 always just worked. No unexplained settings or modes to mess up.