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I'm curious as to how dependent the shared animations and facial flex/speech system are on the standarized bloodlines skeleton.
The shared animations depend upon the bone rigging and hierarchy of the npc skeleton.
Professional Animation tools will use retargeting algorithms to fit the shared animation to the target skeleton.
These algorithms are mathematically complex. The bone lengths need to be the same for the shared animation and the target skeleton. Changing the bone lengths of the shared animation to match the source skeleton may cause the model to look horrible when retargeted and animated.
The source SDK has a tool that will attempt to remap the motion for you. I tried it and it works but extra work needs to be done to get the skeleton to look right. I was not happy with how my model looked after motion remapping. The eyes and flex animations did not match up but the animation itself did work correctly. I abandoned the use of this tool. Perhaps others may have had better results.
If you look at the Troika models, you will see that the shared animations use less bones than the npc skeleton that uses the shared animation. This is of no consequence since the source engine will create a global bone hierarchy for the two skeletons. It will also remap and translate the shared animations for you when the model is animated. The engine dynamically skins the new pose from the two different skeletons. You can see this amazing effect when you let your npc dance in the game.