One can somehow use shape keys for animation, but i don't know how. If someone could tell me how, i can probably add it to the importer and we can re-export imported animations. Though, you can't easily edit imported animations 'cause you won't get bones.
I think it's the exporter that would need modifying. Previously, the importer would import shape keys (the current version does not). When you checked each frame in Blender, the model would appear to have retained its animation, however, when exported, the model would always be exported as the first frame only (in other words, the shape keys were ignored by the exporter). Granted, shape keys would be a royal pain to modify (if possible), but if the shape keys could be exported (and thus would have to be imported again), small changes like swapping a weapon would be possible by simply animating just the weapon.
So I think the first question that would have to be answered is: can shape keys be exported
(or more accurately, can the exporter be tweaked to export shape keys?).