Nagato unlocked his Rinnegan when his parents died!
Madara with Rinnegan can still use Susanoo, and Nagato cannot!
Madara's Rinnegan can drop meteorites, Nagato's can't.
This is what Nagato assumed, Tobi or Madara most likely did it since he didn't keep the rinnegan after that. They must have transplanted the eyes the second time when they saw he would get trained by J-man(using Genjutsu or something for Yahiko and Nagato not to realize) and that would help him gain control over it while Tobi focuses on the eye of the moon plan
Nagato never went through EMS and since he can't cycle through them because it's transplanted, he can't get access to the Sharingan techniques
Nagato can summon huge rocks, he did so against Naruto and Bee... The reason he can't get Meteors sized one is that Madara (Uchiha)+ Hashirama(Senju) DNA > Nagato (Uzumaki)