Remember the part when Nagato uses his Rinnengan Rebirth? The jutsu surprisingly revives every shinobi in the world. You could see all the legendary shinobies like the five previous Kages and other strong ones like Madara himself. But did you notice one of the strong characters Jiraya wasn’t revived! Why?
The Pain’s invasion brought many questions.
This was the exciting moment when Nagato’s Rinnegan’s true powers were revealed, it was during the fierce battle between Pain and Naruto.
When Nagato used his Rinne rebirth jutsu.
Nagato uses his most powerful jutsu to revive everyone he has recently killed at the moment. We can assume that he is not a God so his powers were kinda limited.
Why was Jiraiya left out?
After talking to Naruto Nagato was filled with regret of what he had done, so he tried to compensate for his sins by sacrificing his life and revived everyone he has killed. And Jiraya was a part oh his regret!
Not long before the Pain’s invasion arc.
We all know how Jiraya was killed by Nagato and his dead friends long before the Pain’s invasion arc. Didn’t Konoha even try to find Jiraya’s dead body?
We can assume that…
After Jiraya’s death there was enough time till Pain invaded Konoha, Naruto even went to mount myoboku and completed his sage mode training and mastered it just in time.
It was observed that….
After the full fight we observed that everyone who was killed on the same day came back to life after the jutsu was casted. The extent of Nagato’s jutsu can be defined by two factors, was the jutsu used to its limit or Nagato just decided to which extent should it be applicable?
It’s one way or the other.
We can assume that the jutsu could either revive a large number of people who has just died, or revive one person who has been dead for some time. Considering the fact that Jiraiya had died a few weeks ago and Konoha casualties has been only dead for few hours at most.
It seems as he couldn’t revive all the people.
We can conclude by assuming that he couldn’t revive all the people he has Just killed together with Jiraiya, it was either Jiraiya or Konoha village.