Replacing the Commandos 3D models would be a tough job, mainly because we don't have the tools for this task. As far as I know, the only thing we can do is replacing the textures of the models.
This is hard indeed! I wish I was a modder so that I might help you but we could always try, at least replacing the Thief with the Scout for now then we try the rest (I suggest Commandos 2)