I don't know much about Milkshape's b3d exporter but it sounds like you should try other tools too. Ultimate Unwrap can open and save b3d files; you could try opening your animations, deleting all the polygons, and then saving.
I animate with all the animations in one file, but I don't think Milkshape is useful for that approach; you need an animation tool that allows you to play sections of the timeline, as opposed to the entire timeline every time. I use CharacterFX for animating, although that tool hasn't progressed any in a while so I'm currently looking at Pacemaker and Fragmotion as options to switch to.
That all said, the idea of skeleton-only files for animations would be useful for sharing animations between multiple characters.
I animate with all the animations in one file, but I don't think Milkshape is useful for that approach; you need an animation tool that allows you to play sections of the timeline, as opposed to the entire timeline every time. I use CharacterFX for animating, although that tool hasn't progressed any in a while so I'm currently looking at Pacemaker and Fragmotion as options to switch to.
That all said, the idea of skeleton-only files for animations would be useful for sharing animations between multiple characters.