Well, they're really two different things when it comes down to it. a mini-ITX is a pc platform, while a microcontroller is a well, microcontroller. you add all your pc components into a motherboard including cpu, ram, graphics card, etc, and you can run windows/linux/whatever on the finished hardware and software. The microcontroller development boards i believe you are talking about are really much more basic. You might have additional components like ram or video output, and even might be able to get an embedded linux system together, but you're not going to be able to stick windows on there and play games or anything.