Sati is a program, but was created outside the normal parameters of programming. She was created with no specific purpose in mind, aside form the love between one program and another. She was not created with parameters telling her what she can and cannot do, thus, she can do anything because "she can"...there is nothing boxing her in, so she would be like a new type of program, free of constraints, become, almost human...she can do anything she sets her mnd to.
I've just seen Revo again, and it really is obvious that the W-brothers aligned this story to allow for future projects. There's nothing wrong with that accept that, for my part, it would have been nice to get some confirmation on some of the questions from the series. Fans have invested a lot of time on boards like this one and in their own cirlcles theorizing about the truths and fictions of The Matrix universe and the W-brothers kind of choked with this ending.
Not the fact that Neo and Trininty died, but lets think about what they are really implying here. The Matrix is still in tact. Zion is half ruined but still in tact. The fields in which humans are grown are still there and the machines are still using them for power. Everything is just like it was when the first movie started, only there is a temporary truce between the machines and the humans. That tells us that it will be the next version of "the one" that truly saves mankind and ends the war, and it also says these three movies were almost nothing but an entertaining aside to the real story that is yet to come.