well,
I am a died in the wool IsoPod Addict (
Using an embedded micro is a very good way to augment a PC based system. Unless you go adding cards, writing your own dll's etc, a micro is the way to go.
I see a lot of Pods being used for just this purpose. A little bit of effort, and you can build a dedicated protocol for motion control , GPIO, A/D, other timing , and even CANBUS communications.
Mike