Switching to skeleton that's controlled by ageia?

You have to setup your character with hinges and rigid bodies. Make sure the hinges are all connected correctly.
You don't have to attach a rigid body to every joint. 8-12 hinges should be enough.

Then use the isKinematic flag in the rigidbody so you can animate him while he isn't hit by anything.
When something hits the rigid body, you just turn off isKinematic for all body parts and apply the force to make him fly.

 

Your character most likely contains one mesh and a transform hierarchy.
The transform hiearchy is animated and is what drives the skinned mesh.

Instead of animating the transform hierarchy of the character with animation clips, you drive it using rigid bodies.

Start simple. Create 2 capsules and add rigid bodies to both of them, then add a hinge joint to one of them. Assign the connected body property of the hinge to the other rigidbody capsule.
This will give you the basic idea. Play around with the values of the hinge joint.
Change the spring and the hinge axis etc.


For the character you create rigid bodies for all the body parts. Just by selecting them and adding the rigid body component.

Then you start connecting them with hinges as you did in the small test.

 

Yes. Hinges have a break force. You can modify it if you inspector is set to Full.

Well you have skinned a character in your 3D art program right?

Which means in your a 3D art program you have a bunch of bones.

When importing the character into unity, those bones get converted to Transform's where the Transform's have Animations attached.
So you don't add anything to the object with the mesh but only to the bones of your character.