I would not say Naruto was less suited to fight Madara, because while Sasuke did analyze Limbo. It was not that Naruto could not do the same, it was that Naruto could not actually see what was happening when the Limbo techniques overlapped. Naruto could only sense it.
I have no doubt that Naruto would have been able to take him down seeing how they had to showcase Sasuke's abilities, and then they focused on Naruto's afterwards.
Same with Sasuke though, I see no valid reason for him not being able to handle Kaguya for a while, but seeing how she casually wrecks PS/BM mode, it would become ridiculously difficult.