Animating a 2D 'papercraft' character to move in 3D

I am currently in a small team of people trying to make a 3D game. We have a 3D modeler who doesn't do character modeling or animations and a 2D character artist who does.

I was thinking about how to make 3D characters that are essentially 2D sprite composites move and interact in a 3D world. And came up with the idea of applying the sprites to a composite of flat meshes and having these meshes bend, flex and distort in 3D to interact with the world and also hold 3D objects.

An example of the sort of thing i'm talking about can be seen below:

https://blenderartists.org/t/rig-a-paper-character/572219

And while not quite the same thing or artstyle the world of tearaway illustrates this concept beautifully:

Monstrous creatures would be made up of several 'limbs' that come off of the main body. Such as a winged monster having one joined body and then wings floating off the body. Or a hydra having many heads that move seperate to the body but having 2D bending necks that attach to its body.

The things I need to account for along with the basic 3D bending animation is:
-traditional 2d animation of the sprites while the mesh theyre attached to is bent in 3D (animating face during certain gestures)
-the ability to hold a 3D object such as a weapon while the body carries out a pre-made attack animation (if its premade i dont think IK is needed, just some hold points on the animation maybe)
-different 2D sprite layers that are connected with the main one kinematically in some way (glasses layered over a characters face sprite with an offset, the wings of a monster that are detatched from the 2D layer of its body)
-This one is less of a requirement and more of a "it would be cool to get it working one day" but animated accessories that are affected by physics would be great (such as hair, scarfs, earrings)

Now I know some capital B Basic principles of 3D animation and how they apply to fully 3D animated characters. But I don't know how workable they are for this wierd edge case i'm making. And before I spend hours and days researching something that might not even be good or useful i'm asking the forums for some basic direction. Any 3D animation work would be done in blender and imported into unity.

So having laid out my requirements what should I learn and use to bring this to life?

Would traditional 3D rigging and skinning be the way to go for these characters?
Following on from that what wierd things might I have to do to get the rigging to work well and look good on flat characters?

What topics should I be looking into and researching?

Any help and suggestions are appreciated, thank you for your time.