Hi, ventilator, I think that I got a good idea to get a good second uv-map!

What about using the given uv-map of the textures in MED?

Could you code a plugin for MED, which simple picks a vertex or a triangle of the uv-map, tests which vertices/triangles are connected, stores this mesh, picks a vertex or triangle which is not connected to this mesh, choose all vertices/triangles which are connected to this one, stores it etc.
... this means it takes all the connected meshes as they are in the uv-map of the model, and simply place them side by side, and scales them identically down until they fit into a certain measure of the lightmap.