Thanks for the response.
The main advantage of the boot loader is you don't need a PicKit 3 or U2 programmer after the boot loader has been flashed to the device (you still need to get the boot loader on the target device the first time). New firmware is then loaded with a serial connection. I usually have a MAX232 chip in the circuit for protection, but that's optional. To load the new firmware you just compile/program in Microcode, it will wait for the microcontroller to reset then the new code loads. Depending on code size it takes a 2-30 seconds. Basically the same functionality at the end of the day. Back when I started I used the U2. I would take the microcontroller out of the circuit, put it in the U2, flash, reinstall the microcontroller, test, repeat. After a few hundred times of that I found the boot loader which allowed in circuit programming. It worked fine all this time so I stayed with it.
The cost of the PicKit 3 is about $50 from DigiKey, so I'm going to migrate that way. I'll add the ICSP header on my board then I should be able to use any(?) microchip. I think the technicians will like this since it's USB and the program can be saved on the PicKit 3 and flashed without being connected to a PC.