This really comes down to a matter of preferences, but I've never used the GPIO either. The reason is that a microcontroller board makes a much better GPIO for my use. Then I can unplug it and put it away when I'm done, use it with any PC -- desktop or laptop -- give it away, and carry it into the room where my soldering station is. A microcontroller also opens up the whole world of stand-alone gadgets.

Naturally software / firmware support is an issue. If the stuff you want to do is easy to code on your preferred platform, that's a reason to keep using it.