Here are 2 important things to check in your avatar (mesh + skeleton) before importing it in Godot:
- make sure all scales are at 1,1,1
- ALL objects MUST have their origin at the 0,0,0, including the armature/skeleton
In the latest version of the engine, not checking these points will end up in super weird bone transformation.
I'm working with blender 2.79 and Blender exporter add-on.