Well, I think it's not possible to export the animation without the Mesh because the bones are connected to the Vertices, even if not weighted (but you could try anyway), but I think you should not worry about those few hundred kB we waste this way. There are also some Pros: You could use the same Animation Files for diffrent Chars, as long as the Skeleton is the same.
In earlier times I worked with MD2-like Multi-Sequences too, but then I found it much better to use a File per Sequence. Be it in Blitz, CharacterFX or 3D Studio (I've got an old version). Importing them seperately in Blitz is easy, Load the static mesh first, then use LoadAnimSeq to add Animation Sequences to an entity, then they are indexed from 1 to n.
In earlier times I worked with MD2-like Multi-Sequences too, but then I found it much better to use a File per Sequence. Be it in Blitz, CharacterFX or 3D Studio (I've got an old version). Importing them seperately in Blitz is easy, Load the static mesh first, then use LoadAnimSeq to add Animation Sequences to an entity, then they are indexed from 1 to n.