import bpy
scene = bpy.context.scene

def delete_object(name):
    bpy.ops.object.select_all(action='DESELECT')
    # https://wiki.blender.org/wiki/Reference/Release_Notes/2.80/Python_API/Scene_and_Object_API
    bpy.data.objects[name].select_set(True) # Blender 2.8x
    bpy.ops.object.delete()

meshMap = {}
deleteMap = {}

def clean_objects(skeleton):

    for child in skeleton.children:
        if not  "MESH" == child.type:
            continue;
        dotIndex = child.name.find(".")
        tmpName = skeleton.name + "_" + (child.name[:dotIndex] if dotIndex > 0 else child.name)

        if not tmpName in meshMap.keys():
            meshMap[tmpName] = {}
        meshMap[tmpName][len(child.data.polygons)] = child.name



root_obs = (o for o in scene.objects if not o.parent)

for o in root_obs:
    if "Skeleton" in o.name:
        clean_objects(o)
    if "EMPTY" == o.type and len(o.children) == 0:
        deleteMap[o.name] = o.name

print(meshMap.items())

for meshName, meshData in meshMap.items():
        first = True
        for key, value in sorted(meshData.items(), reverse = True):
            if first:
                print("Keeping " + value)
                first = False
                continue
            deleteMap[key] = value

for key, value in deleteMap.items():
    delete_object(value)