FWIW, if it were me I'd probably go with the Atmel line for a few reasons:
- Generally more resources out there than the PIC stuff. I'm used to much higher level programming normally, so while I'm fine implementing the logic I occasionally get stumped with just what bit of that circuit isn't doing what I think it is, and did I flash that chip with the right bootloader? Having more tutorials and samples out there is therefore a definite plus.
- Ardupilot is based on Arduino, so potentially easier to integrate from that perspective.
- It uses C++, not basic. For me, that's a plus (though for others that could be a negative!)
- From memory, the Atmega chips generally have way more hardware PWM outputs, which you will definitely need with something like a quad.
Having said that, neither chip would be an inherently "bad" choice. They're both perfectly capable. The Arduino's I have are the cheapo <£10 chinese copies (though one actually appears legitimate!) I have three and they've all been fine thus far, one was even left out in the rain for a while... obviously you mileage may vary though.
If you're looking in terms of cost (though bear in mind this will be negligible compared to other quad parts) have a look at TI's launchpad. There's an Arduino like open source IDE for it, so familiar to Arduino users, the low power state is quite frankly ridiculously low (low micro amps range) and you can get the development kit for, including shipping worldwide, $5.
