So Super High School Level Despair, they craved despair right? How Junko enjoying being executed because of the despair coming from it?
The way Nagato craves hope, how he wanted to kill so he could show that hope can win against despair. Which is basically the exact opposite of what Junko was like. Wouldn't that make him SHSL: Hope? And who was granted that same title in DR1? Makoto. There has to be a reason for that connection.
The whole Nagato = Makoto thing is a bit to far fetched for me, though it was my original thought, it may not be completely true, but there is a connection there. And the theory about Junko that had been going around since the beginning of DR! ended up true.