That is a major concern for me as well, Michael. I made those animations as a test, so they are quite bad. But they use an alternative model, a model which is previously dismembered, cut in half, or whatever you need. This is not good, because you also need an alternative armor model, which is perforated or whatever is needed. I can't think of any other way to do it, so It could require a lot of work.
About the 3D and the environment, I think they fit very good, at normal zoom, they seem to blend nice with the 2d critters.