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.)