https://www.youtube.com/watch?v=VkMU1mKdwPI This is a very very interesting theory, and I've gotta say I'm on board with it.
My favorite fan theory about the Matrix was that the "real world" was just another level of simulation, to keep the humans content with a supposed struggle and victory. And if the Machines were advanced enough to make a single matrix, there's no reason they couldn't double-down.
That is an interesting idea. I've heard it float around a few times. It would explain Neo's ability to manipulate the machines outside of the matrix.
You're over complicating. He was connected to them the whole time, all that hardware throughout his body allowed him not only to communicate with them while he was in the matrix but also outside of it. Neo sacrificed himself so that both species will finally make peace with each other. Regarding the One. What most people miss is that he wasn't only the savior of mankind but also of the machines. That was the prophecy! The machines in their pursuit of revenge toward humanity got trapped by their own invention. They had no way of protecting themselves from Agent Smith just as the humans in Zion had no way of protecting themselves from the machines -- once out of the Matrix he would have destroyed everyone human and machine.
I'm kinda still with MattPat on this one. I mean Neo could do like two things in the matrix, and he barely even did those two things. He could stop bullets, and he could fly. Everything else he did was stuff any of them could do. Smith on the other hand literally recreated the entire matrix in his image and assimiliated everyone into it. I think one of the two of them clearly was a little better at the whole 'manipulating' thing.