Where in Naruto did it say Madara had Amaterasu and Tsukuyomi? Nagato can repel Amaterasu but does Madara have Amaterasu? Not all Mangekyou Sharingans have that techniqueLet's say Nagato. Shinra tensei can repel amaterasu. I'm not sure about tsukuyomi, but we're talking about rinnegan wielder here, he could probably somehow counter it. Susanoo, well I think chibaku tensei or large scale shinra tensei could do quite good against it. There is also fourth dojutsu that comes with EMS which is still uknown, but for now, I'll go with Nagato.