I'm 4 and a half years late on the reply here, but in case anyone finds this looking for similar answers, this process started to get me somewhere:
- Import your fbx animation into a new scene. Select all the bones and go to the Animation menu > Save Animation.
- Back in your character scene, select all those same bones and go Animation > Load Animation. Find and select the animation file you just saved, and then click the Edit Mapping button. You'll get a window where you can choose what tracks get imported.
- At top in the filters, uncheck everything except for the Transforms for position and scale. In the center column, which shows the things that are being taken from the animation, select the first thing, then hold shift and select the last thing to select all the position and scale stuff. Go back and find the Hips/Pelvis (and any IK controllers or things that need position) and ctrl+click them to make sure they aren't selected. With only the unwanted position/scale things selected, click the right arrow button to remove them from the animation transfer. Save Mapping so you can skip the setup next time.
- Replace or Insert the animation at a certain frame, select Relative or Absolute initial pose, and click Load Motion.
Note that if your legs change length, the feet will float around even if the animation got imported perfectly. For standing animations I had some luck locking the feet down with IK constraints before loading the animation, and then animating any foot movement manually.
Another solution could be to keyframe everything on your rig on frame 0, then Load the animation by inserting it at frame 1. You could then manually remove any scale and position keyframes you don't want using the graph editor, leaving them at whatever they were on frame 0. Maybe?
