Animating and creating pose libraries without Shape Keys Allow me to properly explain, step by step, in order for everyone to understand the question.

In case anyone who reads this is unaware, Manuel Bastion has released an add-on named "ManuelLab". This add-on creates Humanoid meshes you can tweak however you please. It's finalization feature uses Shape Keys.

Meanwhile, Karan Shah has posted tutorials involving creating Motion Graphics without Shape Keys or Add-ons. He also has a tutorial involving 2D cut-out characters...without Shape Keys...and with a Pose Library.

Please, do not get me wrong, I understand 2D and 3D are 2 completely different things here, especially with how Karan Shah uses the NLA editor. However, I want to set that fact beside the question at hand.

Is there any way to finalize ManuelLab generated Meshes, with their skeletons intact, without using Shape Keys? I believe there is something to be gained from the mixture of what both of these artists and developers have created. This sounds like a tall jump or too steep a step, but I am no less hopeful.

The pose library involves the use of multiple layers to Move objects throughout.

Edit by request:
http://www.manuelbastioni.com/download.php
http://tutsplus.com/authors/karan-shah
http://www.tutsplus.com/authors/karan-shah (Check the 1st 4 tutorials at the top, at the time this post is edited.)
I think the answer is simple : you may need up to one bone per vertex to obtain the same accuracy as shape keys.

About Karan Shah : he uses UV warp modifier which is purely based on the UV mapping. So that does not change the 3D (or 2D) geometry. Also, in this approach, you cannot mix the effect of two bones (and shape keys can be mixed).
If we want to compare shape keys effect on the face of a Manuel Lab character to UV warp effect for Karan Shah, you'll see that for each shape keys combination (for ML), you may need one texture part (for KS).

After that, maybe something new could be invented... I don't know.