[Theory] Tobi met Nagato after Jiraiya Left

[Aze]

That seems too convenient. And isn't the Uchiha Memorial in Konoha? How would they get in without causing some ruckus?

Tobis Space time ability allows him to enter every place on the planet without triggering the barriers.

 

[Inception]

Well...What I was suggesting that they didn't know about Nagato at all until they heard about him and his Rinnegan. In other words, instead of actually transplanting the eyes on him maybe Tobi was being metaphorical. Maybe he meant that he helped unleash the real powers of the Rinnegan by instigating and causing Nagato to go into crazy mode.

Sounds the same as when Nagato's path instigated the manifestation of the kyuubi in Naruto back in Invasion of Pain.

One of the things I am getting at is how in the world would a ninja like Madara/Tobi know about Nagato? I doubt they saw him and said, "This kid has the Rinnegan". There has to be a situation that they heard about it and then decided to act. It may have been a mere whim by a dying Madara to leave his powers with Nagato.

Tobi did help unleash the power of Rinnegan by sending the ninja after them. I am guessing he was chosen because Uzumaki are known to have strong chakra and life and this might just be a requirement to use Rinnegan to the full potential. He is somewhat similar to Madara in this sense. As soon as Madara came out of the Edo coffin, he exclaimed that Nagato managed to grow up. This kind of proves that he gave the Rinnegan to Nagato and was expecting Nagato to use Rinne Tensei to bring him back (as explained by Tobi).

We know that Rinnegan comes after EMS confirmed by Kabuto/ Orochimaru and Madara. How can an Uzumaki develop a Rinnegan when he doesn't even have the EMS to begin with? He can't! It was transplanted. Madara is obviously the original user as he can activate and deactivate the Rinnegan at will. We know the opposite is usually the case in people with transplanted eyes. This also explains why Tobi claimed he "gave" the Rinnegan to Nagato.