Look, i'll shed my ideas on this, and some answers thanks to a god damn helluva lot of looking.....
Neo.
As you may have noticed near the end of Reloaded, he stopped the Sentinels, and proclaimed "I can feel them". The architect did not want him to go out that door, when he did, he exited the matrix, and knew that it was a bomb flying at the Nebuchanezzar, when no-one else did. Somehow, in real earth, he has become "The One" in both worlds, his power has crossed over, and he can stop machines. But he needs to learn to control it before the diggers get near Zion.
Agent Smith.
After replicating himself into another real person, and not an Agent he exited the Matrix with a different identity. He was the only one who survived through the massacre of the 5 counter attacking ships.
The Architect.
The creator of the Matrix, the most confusing bastard on earth. (so to speak). And if you didn't notice, he wasn't at the source, it was control room, kind of. "The function of the One is now to return to the source, allowing a temporary dissemination of the code you carry, reinserting the prime program. " Neo hasn't returned to the source. Biggest Bullshitter.
The Oracle.
Told Neo that choices were already made, just needed to understand why he made them, and what he had made. Most importantly, where the hell did The Seraph take her?
Councillor.
He's a program that escaped the Matrix, Smith ain't the first. First of all, he has a voice that is the same as Hugo Weavings (Smith), Secondly... "I hate sleeping. I figured, I've slept the first eleven years of my life away, so now I'm just making up for it. " and earlier, Smith said this :- "Mr. Anderson. Because of you, I'm no longer an Agent of this system. Because of you, I'm unplugged. A new man, sort of speak- like you. Apparently free." How long had Agent Smith been in the Matrix?
Zion.
Nowhere in the film did it say that Zion had been destroyed, we got told it would be destroyed if Neo stepped through the door he did. Yes, 5 ships were destroyed, but Zion wasn't.
What I think will happen.
I'll probably be quite off the mark here, but nevermind. Agent Smith has learnt to replicate himself (check above), but take the looks of the others while outside the Matrix. If left to his own devices with Neo, what the hell do you think he's going to do? Thats where the 2 Neo's come in. The ending of the trilogy, comes down to a fight between Neo vs Neo (Smith), for the destruction of the Matrix or Zion, one has to go.
But mainly, remember this. Revolution, a full circle, to come back to where something began. Goodbye Matrix, welcome back all humans, Zion's going to take some growth spurts.