There is no way he could or would ever open all the pods.. imagine all those billions of people with no structure of a civilisation to support em...well, it could happen but it wouldnt be a very happy ending.

heres some of my thoughtz:
Neo is now beginning to really free his mind.
remember gets given the bent spoon by that over enthusistic gimp-boy, its from one of the little bald kids (from the oracles flat in the first movie) and its showing him that the matrix was a key to unlock his perceptions of reality and give his sub-concious mind the confidence to distort reality to its own needs, as it can do in the matrix.
To the mind the matrix is a reality, it contains sight, smell, touch etc, so the way neo has trained his mind to interact with that reality has translated into the real reality :roll: .. if that makes any sense..
Its all a bit lawnmower man if you asked me, but obvious it was going to go that way..

The other thing i think could happen ,like ZM says is 'reality' itself could be part of the matrix, and both what they percieve as the matrix and thier 'reality' could be inside another, real matrix or even in a computer game in a normal reality or somthing, **** knows.. there has to be another twist coming in the story.
If this is the case i dont think they are still in thier pods though because if they are still in them, and just dreaming it then why is that any different to the billions of other poeple in thier pods dreaming about going about thier daily human lives - surly this is just as valid a source of randomness as anything our heroes are doing