blender-retarget
                                
                                 blender-retarget copied to clipboard
                                
                                    blender-retarget copied to clipboard
                            
                            
                            
                        Automatically align target armature along with source one
In #15 the add-on started to understand the model hierarchy, so, it'd worth a shot to try to automatically rotate target bones to make them aligned with source ones. Also, consider to automate other useful transformations, e.g.: scale and move source model.