Board Thread:Theories and Speculation/@comment-3001903-20151205022433/@comment-734582-20151205130232

Elveonora wrote: Maybe Nagato had years to adapt to Madara's eyes? I think it's this.

Nagato is a natural Uzumaki. He was unable to access the full power of the eye for a long time, which protected him from the damage it would otherwise do, while his heritage provided the necessary strength to wield the eyes normally. Besides, whenever he did use the power (e.g. when his parents were killed) he fainted thereafter whereas Obito did not. Over many years of barely using the eyes he simply grew strong enough to wield both eyes fully (again, he did not seem to access higher powers until after Yahiko died) whereas Obito tried to use it fully from the start (and almost died because of it).

So simply put, Nagato grew into it over the years, while Obito tried to master one eye in an afternoon.