Finally added some new features, some polish on the code and updated the script on github. You can use it to retarget any amount of animations over your characters without much hassle. You can download it here.
You just need a scene with an already characterized character and a folder with animations in .fbx. The animations need to be either already characterized or not. If they are not, they need to be on a tpose on frame 0 and have either Motionbuilder (with or without a prefix) or 3dsMax Biped nomenclature. They need to be characterized to be retargeted from one control rig to the other, so that’s why it needs a tpose. For a custom bone mapping you can easilly add a new one or edit the mobu one.
I might add bvh support in the future (maybe with FBFileBatch()?) when I find more free time again. Or feel free to add it yourself.
* edit: Ok, added support for bvh, namespace, and custom skeletons. You still need to edit the bone mapping if you have custom skeleton though.