I think it's mainly to do with the Tools namespace. Why not build it directly into the main Haddd class? So instead of importing a mesh using HImport.Haddd.Load, make it Haddd.Scene.MeshObjects.Load? or Haddd.Import.Load?
Do you think it would be better seperate the material portion of the .haddd files into a seperate material file? Maybe a .material file? That way it would be easier for someone to load the same mesh but with different textures using external files. Of course it would mean there would have to be an extra line of code to specify the material file... But shouldn't be that much trouble if you just put it as Mesh.LoadMaterial(string) right?
Another thing is, at the moment, we're creating a material array whenever we want to assign a material to a mesh right? Would it be a better idea to make it a list instead and have users create a single material and add it to the mesh.