Using little robots to speed up the stop motion animation process
Your idea sounds absolutely possible. On the other hand you write that you have never done any stop motion. 

I think it would be very well advised to start with some basic techniques (by hand) and then see what you can maybe automate in the future. 

Building puppets that can be easily animated is a already a complex task, since it usually involves building metal / wire skeletons etc. so I'd slowly approach the overall complexity of the matter and then advance to the next step.

Some introductory reading to get you started: 


Stop motion - https://en.m.wikipedia.org/wiki/Stop_motion
Go motion https://en.m.wikipedia.org/wiki/Go_motion
Pixilation https://en.m.wikipedia.org/wiki/Pixilation
Claymation https://en.m.wikipedia.org/wiki/Clay_animation
Animatronics https://en.m.wikipedia.org/wiki/Animatronics


I think what would more sense is to follow the idea mentioned by Adam Mann Pro using some basic animatronics.  If you build a remote controllable face for the puppets which allow you to easily setup facial expressions, that would speed up the animation process immensely and is in itself already very complex. Here is an example of an animatronics head from the movie "the world's end":