I do not use the animation features of either of these tools (currently). I have used MotionBuilder to clean up mocap data and to create new motions in their story editor.
Are there any animators out there who have experience doing NLA animation in both of these tools and whether the current version of Blender is a viable replacement for MotionBuilder in terms of its NLA animation abilities. (For cleaning up mocap data our animators have access to another tool, in addition to MotionBuilder.)
…a bit more searching and i found this wiki page:
http://wiki.blender.org/index.php/Competitive_Analysis/Animation_And_Rigging