So, character animation has never been a breeze - in any format, although I'm specifically addressing 3D character anim here. Whenever a client approaches me and asks me to give life to his new puppy, the line "OMG, rigging.." immediately pops into my mind. No matter what solution or approach you use, the only sure thing is that you'll run into trouble. Fact is, no 3D application does it all as efficiently and cleanly as if you use multiple tools, but when you go down that path you inevitably add the darned "conversion" issues to your pipeline. Either your 3D applications have different conceptions about what direction the Y axis points to, or Motion Builder wants you to rotate your character 180 in the Y axis (wait, or is it Z?) - what will inevitably break your rig no matter how simple a "180 rotation" process sounds in theory.
Be it import/export conversion, rigging tools or advanced shading, high-end features are always like that. They cater for a very small share of any company's user base, and receive a proportional attention - read, investment - in terms of proper functionality and support.
Probably just how the economics dictatorship makes things go, but you know what's the most curious thing? We artists rarely account for that when we estimate our schedules, no matter how spanked we traditionally are by such processes. Go figure.
