Board Thread:Theories and Speculation/@comment-43776375-20190921063938/@comment-32685487-20190921180412

Nagato's body was messed up because his life force and chakra were being used to control the Gedo Mazo by syncing to it(he didn't know there was another way to control it, as Sneaky Obito didn't tell him) and as shown later on if Nagato absorbs a large amount of chakra he can use the chakra he absorbed to restore his body(vs Itachi, B, and Naruto). For plot convenience, in life he remained synced to the Gedo Mazo so that wasn't possible.