Will it depends on the Jutsu you know.
When we compare Naruto in Sage mode vs Madara. Naruto may get a shot with his shuriken but the perfect Susanoo should win. simply because Naruto lacks in a number of elements in Ninjutsu. He can't use wood, earth or water to make some creature which would be able to fight against Susanoo. But he can summon Gamabunta or some frog.
Will depends it knowledge in ninjustu lacks Eternal EMS.
If the Shinobi has knowledge of a sorts of Jutsu Eternal Sage mode.
A Sage jutsu user will surpass and EMS user eventually.