DataCrypt:
Since a board like the Uno uses 2 Atmel mcu's (one for the USB and one for the program), if I was building my own PCB - do I need to program that USB mcu with any special bootloader or program?
yea there is a program on that chip that does the USB to TTL serial conversion, though you could replace it with a FTDI chip or a MCP2000 (which is more or less a pre-programmed for USB to serial pic), or heck if your computer has a RS232 device a few parts and a couple transistors would get you by (I used a dongle with a couple zenier diodes to clamp voltages, and a hex inverter for years before my current "bench" machine cheated me out of a serial port)
on regards to PIC vs AVR, its a ford vs chevy debate, AVR does more per cycle, PIC's seem to have more options, though more options means more decisions lol
I think the .net stuff works on more powerful chips, but its a much heavier programing system so performance and memory consumption would be something to look at. PIC32's are also in about the same price range as arduino and offer BASIC languages that run on the MCU itself (like stickOS basic)
I have a PIC32 with stickOS loaded on it, due to the overhead its actually about the same speed functionally as an arduino ... even-though it runs at 32 bit 80MHz (vs 8 bit 16MHz) though it has half meg of storage and 96-128k of ram. That being said it would kick the crap out of an arduino if programmed with some low level stuff, I have owned it for longer than my oldest arduino and have never really made heads or tails out of 70% of it... (and most of its software is windows only which puts a kink in my linux bench machine, that is just screwy enough to crash windows constantly ... stupid dumpster computer)