Just watched part 3. Quite good imho. But seems a little rushed, as if the bros were trying to beat lotr screening. Anyway, on to the theories....
Why smith can fly?
In Part 2, Smith said some parts of Neo copied onto him as he was killed in Part One. And so he became what he was. But he did not know how to fly then. The Oracle in part 3 also confirms this that he was the opposite of Neo.
Is Neo dead?
I think in the end of part 3 he is dead... as a human anyway. He was used as a conduit by the machine so that when he was infected, the machine could use Neo to eradicate Smiths. In any case, trinity was dead and there wasn't anything much that he waned to live for.
Who is seti?
No idea... i think she is the product of the 2 indians. But she was not created by the machine and so has no real purpose in the Matrix. The station was a void between the Matrix and the machine city. And so she was temporarily safe there. The Deal with the Oracle was to bring her to the Matrix to let her live. The only way is thro the frenchie's smuggle machine. WHich I suppose he uses to transport werewolves, vampires and sprits from time to time..... Besides, being a program without a purpose, I guess the Oracle thought her the ways which the rest of the kids in her room did in part one.
The Spoon!?
The spoon was used by a kid in part one. Who is the kid is anyone's guess. The spoon in the real world is not really teh same spoon and the "nerd" (rightfully named "the kid" from animatrix) simpy passes it to Neo symbolically.... btw animatrix tells you who this guy is.
Is Zion another program?
No, its real. Part 3 made sure of that.
Now awaiting.... LOTR!!!!