Where exactly is the problem with the size of the md2? Storage space or main memory usage? For a keyframe file format, MD2 is already pretty good for storing the files. In main memory, size will be the same no matter which file format you are using. If it's too large, maybe reducing the number of keyframes is an option?
Do you want to manipulate the vertices after loading? If so, you can do this by implementing an IVertexController. However, this is pretty low level and you have to know want you are doing or otherwise you'll screw up the model. In addition, it actually meant to manipulate Object3Ds' meshes, not those from animations. To make the animation meshes accessible, you somehow have to feed mesh after mesh in a kind of dummy Object3D. So yes, it is possible but pretty awkward.