there's a lot more that can be told. what happens to the people in the Matrix now? they can't all be freed at once instantly - they could die from shock (people are not removed from the Matrix after a certain age, remember?), run out of natural resources for a huge population, cultural unrest, etc. hardly what i call a happy ending.
there could be scores of stories that don't involve Neo or Trinity. there is a whole world out there that could be explored. after Macross was Macross Plus, Macross 7. they told more of the Macross universe without basing the story on the original characters. the same can be done in the Matrix universe.
also, remember that it is implied that peace will not last - and how could it? the Oracle also implied that Neo would come back, probably as another "One" - which means that the whole process may yet repeat itself again, maybe a little differently this time. a lot can still be told. of course that doesn't mean that it should be told. people tend to mess up sequels. that's why i'm torn. i want to know more, but at the same time i like keeping it open-ended.
either way, an evil cyborg Neo wouldn't come until at least the 8th movie.