You can put tracking marks on someones face, then track them, then apply the track to shape layers in AE. It's not motion capture, it's motion tracking. Mocha would be a good tool for this. The key to success is careful planning and careful photography. I don't have a link off the top of my head to point you to, but if I think of one I'll send it along.
As Rick already pointed out, you do tracking, not capture in AE. "Capture" would imply that there is a fixed reference structure that can be associated algorithmically. What you want to do is perfectly possible in AE without spending any money, it just needs to be set up accordingly and of course there will be limitations here and there, requiring manual work, but it's not that it can't be done at all... E.g. you could still easily track each point and then use scripts like Tracker2Mask to have a mask shape follow them. And of course if you are willing to spend some money, this can be expanded by using other tools... I for instance have developed a setup for a client using FreeForm Pro...
Thank you very much for the information. I am watching some tutorials on both of those ideas right now and I think this might work for me.
Thank you again.