Yes, but you don't apparently don't believe it.
One $5 PIC chip can have >30 i/o pins that can actually supply a usable current (25mA) and that won't burn out at the drop of a hat. At any rate, parallel ports are legacy devices coming to a rapid demise. Why do you wish to make your device of the future rely upon hardware that will soon cease to exist?
A bunch of micros now have USB interfaces in them. FTDI chips can take up the rest of the slack. I think it's safe to say that USB (and possibly firewire) are becoming the defacto standard interface to most external devices attached to a PC.
So what, you already have one present, why not use it? Many ITX boards have a connector right on the board to let you hook up to it. They may call it an SMBUS connector, but it's compatible with I2C.
I don't think assumptions are an option and frankly I'm surprised you would ask such a thing.
I really don't understand your motives. You come here asking for advice and then you go to great lengths to refute every bit of it, including building straw man arguments and then burning them down. Outside of being a troll, I don't know why you'd wish to do that. Many people, with far more experience than you (or I), have told you the same thing, "keep your ITX board for central control and functions that requires high CPU performance or floating point math, but offload as much as possible to "smart" circuits that can actually do a better job." AFAICT, nobody told you that you should use a micro in place of the ITX board nor did anyone tell you that your idea absolutely would not work.
Whether you believe it or not, microcontrollers running at 4MHz have abilities that a 1GHz ITX PC platform system cannot duplicate even with an RTOS. Interrupt latency is the first thing that comes to mind. Then there's i/o, PWM, ADC, CCP, comparators, timers, various serial comms etc capabilities. Microcontrollers are intended to be the magic glue to interface digital electronics (like your ITX board) to an analog world. How could you conclude that everyone got this part wrong?
BTW, could you post a link to the "$50 IO board" that you refer to? I'd like to examine its capabilities.