Here is my theory, based upon all the junk I have read.
Neo is in the Merovingian’s control. Morepheus, Trinity, possibly Seraph and others have to fight Merovingian and his posse to free Neo – this is the Club Hell fight. Eventually Neo is saved. Neo eventually gets to the “Speaking Machine” or whatever it is called, at 01 because that is where they believe all this is supposed to end. The Speaking Machine explains that it is losing power and control of the Matrix and the machines to Smith. The only way to save Zion, save the Matrix (yes, save it) and save them all is to destroy Smith.
This leads to the Neo vs. Smith fight. At the same time there is the Machine vs. Zion fight.
Once Neo wins, he gains control of the Squiddies – or the Speak Machine regains control of them, and the fight with Zion ends. (An out on the limb prediction - the same thing that lets Smith exist in the real world leads to his demise. He will bleed or something and then realize he is now mortal. This will lead to him being killed with a knife or gun or something “simple” like that.)
Neo then has to give up the source code to save the Matrix. Only, part of him becomes infused with the whole system leading to changes. (There is a chance that the Neo v. Smith fight comes first, then a fight with the Speak Machine, but I only give it a 30% chance.)
In the end, the Matrix remains. Although there is a chance that it will be more open and people will have an ability to choose it or the real world. Zion, although damaged, remains. An uneasy truce is formed between the machines and Zion. Several lessons – Follow your heart, you make your own choices, have faith in your beliefs, man is dependant on machines (and vice versa), if you build it they will come (oops, wrong movie) come from the movie. None of the “Answers” will be written in plain language. The film will end with several open questions, several different possible interpretations (such as is the Archy good or bad, etc.)
Neo – probably lives
Trinity – I’m guessing she lives
Morepheus – Dead
Councilman What’s his name – Dead
The Kid – dead
Niobe – Lives
Commander Locke – Dead
Oracle – I guess she lives, and will go out on a limb and say she reverts back to her original form
Link – Lives – he’s not allowed to die after that speech in M2 plus the good luck charm his wife gave him.