Nagito's a better antagonist than Junko.
I'd agree with that.
Junko, while great, feels like something of an unstoppable force of nature or an idea.
With Nagito, you see the gears turning, and you know there's something terrifying behind his friendly smile. He's a person would who doesn't fear death or pain. He would not hesitate to slice himself or anyone else open for his beliefs. Peeking into his mind really does seem like it would be stepping into calm, collected madness.
Can anyone clarify if Nagito knew it was a simulation? I thought he did based on the Hope's Academy file. His reaction right after was very strong and I do believe it mentioned stuff like Hiyoko's growth spurt and maybe some of the body alterations the Remnants did that wouldn't be reflected in their avatars. But I may be way off here. If he knew it was a simulation I can definitely see him surviving or recovering before the others would.
I don't believe Nagito knew it was a simulation. Nagito didn't even know who the traitor was. The point is that he was always a nutjob, even before becoming an Ultimate Despair. This is why he viewed all of the others with such disdain after reading the Academy file. He discovered they weren't symbols of hope, but symbols of despair... himself included. Which is exactly why he wanted all of them to die (including himself) so he could transcend and become the Ultimate Hope.