Congratulation, a day of work what needs a second with an Arduino IDE. Now the Microchip CEO has to make another funny answer video
Would be better if they would fix the thing.
I like PICs, but PICkit 3 is terrible. PICkit 2 was fine, no problems with MPLAB. The new MPLABX is bloated and slow (it is based on Netbeans, written in Java, which itself is not that slow, but maybe all the custom Microchip plugins slow it down), and all these PICkit 3 target specific firmware is silly. The programmer itself should be dumb, they should put all the logic into the PC side. Recently I tested
a new project I'm developing with a Lattice FPGA chip, which can be programmed with JTAG, and their programmer just uses a FT2232 chip, so you can build your own programmer easily. Yeah, I don't like the FTDI business practice, bricking fake devices, but they are the market leader and they do all the stuff for you like driver development, which is integrated in the Windows update etc. and you get an easy to use interface for low-level GPIO control, including some interesting high speed FIFO and JTAG modes, and UART.
For projects where I don't need the smallest, cheapest microcontroller, these days I just use a modern ARM microcontroller, like the nice LPC family microcontrollers from NXP. It has a USB port with a special boot mode. Just plug it into your PC, it is enumerated as a thumb drive, copy the new firmware to it (which the special boot loader will flash then very fast) and you are done.
Everything should be as easy as possible, like with the Arduino or the USB thumb drive firmware update process. Now the question is: Will this get more difficult with Atmel chips and more bug-ridden when Microchip buys Atmel?