I was happy with the ending as was. My only hope for any more Matrix is because at the end I just thought, "Oh, damn, it's finished now".
I certainly agree with the possibilities of the binary system, that is all clear. And the possibility of Neo being a program, that too is a fairly apparent. In fact, the Architect says it himself in Reloaded, telling Neo of the designs of his five predecessors.
I think there is possibility of the 'real world' not being quite so as well, but I am unsure as to whether the brothers actually intended that route as such. I feel that in there wish to open it up to a wider audience, those who wouldn't pick up on certain things, that they may have to some extent made it such an open possibility. If so, I am not sure that it was intended for certain, but an open choice to be made by the viewer.
That's one of the things I liked about it, it took a Donnie Darko type view of, 'you work it out, and what you work out is one possibility, but not the only one'.
A small thing yes, but I don't believe the people who can be freed from the Matrix now are those who accept Neo, I think it's just those who become aware that they are in it. As in the first, it was said that some people refuse to accept it, and only those can be freed.
Although, having said that I'm beginning to agree with you, since I think, from the end, that Neo is essentially the Matrix now. I think what the machines did to him at the end, giving him that quantity of power, diffused him throughout the whole of the Matrix, allowing him to defeat all the Smiths from within. And that's why he's not actually dead - as the Oracle said, she expects to see him again.
Well, there's about a million other things I could ramble on with, since the amount of sheer information, and references in the films go on and on.
But suffice to say for now, I was happy with it.