During my first playthrough of the game, I actually believed that Makoto and Nagito were actually the same person. This was based on their character designs, Nagito's assumption that Usami's appearance meant a killing game would start, and several times later in the game where Monokuma says that Nagito reminds him of him, the him I assumed being Makoto.

However, upon doing some reading online, I learned that Nagito was based off of the idea of a deconstruction of Makoto. Whereas Makoto is affected by luck to some extent, Nagito has lived with a cycle of extreme good and bad luck throughout his entire life. This cycle has caused both his obsession with hope and his bizarre behavior and thought patterns, whereas Makoto (who never had such an extreme luck cycle) is a normal guy with a strong belief in hope. In addition, Makoto's belief in hope is ultimately what pulled everyone to together, while Nagito's belief in hope is what pushes everyone away from him.

My guess so far for what is going on is this school is actually a simulation

That is correct. When I learned about the simulation for the first time, I believed that Makoto had created Nagito as an avatar and was only pretending to be the way he was to throw off anyone who might be an ally of Monokuma. In reality, the DR2 students were put into a simulation by the survivors of DR1, mainly by Makoto. Why? The students of DR2 were part of Ultimate Despair, and are referred to as the Remnants of Despair. The simulation was designed to rehabilitate them from Junko's influence. However, one of the students uploaded an AI of Junko into the program, and before going under, the Remnants agreed to a plan where AI Junko would take over their bodies if they died in game, since they would believe that the sim was reality, and thus, they were dead in real life.

Makoto Naegi da !

That was actually a coincidence on the part of the creators.