...in my case it was Troy and Cube 2. I didn't even know about Cube 1, but it seems that there are awesome special effects.

Ok, from here on it's SPOILERS

I think you missed the point of Peace. Peace, done correctly, would allow you to cooperate and advance. Humans and machines could come together and try to bring back the Sun. And then there may be plants. Maybe even rivers. And then maybe the machines will need to farm humans no more.

As for the Matrix from now on: The architect says that the Matrix will continue, but anybody who wishes to leave, will be able to. What does that mean? This means, to me, no agents, and anybody who wishes to take the red pill, doesn't have to go through heck to do that.

What's the point? Well, the point is exactly what it was in Matrix part one: living in the truth. Wanting to be free, even if there is a price to pay. I know that I would definitely choose the truth over illusion. Indeed, there will be many who will prefer to stick to the illusion for psychological reasons. But those who seek truth, will be able to achieve it. And maybe those who regret their choice will be allowed back into the Matrix, without needing to betray their friends.