Shape Animation Tool 2.0
At least I updated this tool.
Main feature is layers. Now deformation can act independently and with different keys.
Overview of the tool you can see in videos from previous version.
Also I place the good sample of the using another tool with similar method, as I think, in Hotel Transilvania after 1:35.
You can buy this tool from this site for 20$.
Free version 1.2 is available also in creative crush.