hey
at first i wanna say custom material be created for remove standard material limitation.
so it is not the alternative way for the shader material that is just for customization some papular material for easy use you can see the custom part in the CustomMaterial Samples
so if you wanna use the easy way that can be exist in any new standard system and we try support that
also we have NodeMaterial as good tools for making shader
at least the shader material is always the G(old) way can handle any advance system
** if you wanna use the shadow and lighting of Babylon system the best option is using standard material and you can append any kind customization with custom material on that when you need .
also i have shaderBuilder the different looking for the material system
cheers
R.Nasimi