I thought about doing a design like this, but instead, using a design like the old K150 programmers. Due to the lack of working software in linux, I kinda abandoned the idea. Its something to think about bc it has dc/dc converter for 12v and everything built in, no need for external stuff, but the software is the real issue.
Neat idea for your programmer btw, a little observation is that your using a seperate 5v regulator, why not just use pin 2/5v out on the rpi? The pic chip uses a few uA and maybe a few mA at most, so it wouldnt even be any drain tbh. No use reinventing the wheel and it'd cut down on cost to make it/parts.
The 12v, you can maybe use a seperate chip to run as a pwm generator to use a buck/boost converter to convert the DC up to 12/13v needed, then you wouldnt need any external regulators or anything like that. Just make it into a self contained shield for the rpi and it'd be good to go for your projects. I believe roman black has a buck/boost converter that just uses like 2 transistors and some other components to raise the 5v to 13v for the chips.http://www.romanblack.com/smps/conv.htm
There's the converter I was talking about.
Edit: Just a question, why use 6v dc when most chips can only handle 5v?