ARK lore expansion
Okay, I know the game didn't have the ARK properly thought out, so why don't we do it instead?
The first issue everyone has with the matrix is that they know they are inside the matrix. Make it so that you don't know that you are in a simulation. Just like the one you are in right now ;)
Make the Ark's inside to be procedurally generated. Virtually infinite so it never feels like a prison.
Make the satellite in a way, that can interact with the outside world. Land on places, self repair, get fuel, improve it's own hardware. I image it to be more like the grey goo rather than a satellite. And make it travese the universe. And if it encounters any sentient life-forms, stealth scan them too and add them to the simulation wile also leaving the 'real ones' intact.
You can't create the perfect matrix without extensive testing, it will need to be updated from time to time, in order to do that: Create a janitor A.I. With a mix of every habitant's own brain scan that is removed from all human needs (boredom, requiring social interactions, etc) and make it so that it can monitor the well-being of the habitants and make reasonable adjustments to the simulation and create content if needed. So basically a benevolent A.I. God that knows you because it IS you.