Finally had a bit of time to try out Live2D. I had seen it used in games for characters with flat shading, but I was curious to see if it can handle photos. And considering that this animation was created from a single photo, I'd say that the results are very promising. I can certainly see myself using it to complement stop motion in shots where fine movement or mesh deformation is needed.
There are two downsides that I can see, though.
The first is time, as setting up even a simple rig like this took more than a day. So it's definitely not feasible to use it in shots with camera movement.
The second is cost - at $240 it's very expensive to use for non-commercial projects. It does have a free version (which I used for this anim), but that is limited to 720p, and does not normally have the new mesh deformation algorithm (which is its main selling point). Unfortunately the only alternative I know (Spine) is even costlier.
As if making stop motion wasn't already costly enough...
Note: the original photo is of a non-posable figurine of Senran Kagura's Mirai, from Griffon Enterprises. It was shot with an EOS 450D and Tamron 60mm f/2 Macro lens.