What app are you using to create the .obj file? If your using Blender you can export to the Animation (with alpha channel). Bring that into Motion. (Set the anti-aliasing to 16 and check the full sample box. Go and have a few cup of coffee.)
I have script that allows you to export a Blender file to Motion. I haven't figure out how to use it. (I need to ask that question in here.)
Blender and Motion 5:
You can bring a .DAE file into FCP X with the "3D Supercharger V2" plugin, which will soon be coming to Motion, with major updates in a month or two, from what I'm told.
It is all done through Quartz Composer.