The trilogy was always meant to be a trilogy.
The brothers refer to Reloaded as Matrix Squared and Revolutions and Matrix Cubed.
The whole trilogy is about the Journey Of The One.
Just as George knew Vader was Luke's father from that moment he first stepped out of the smoke and throttled the rebel before capturing (his daughter) Leia, the brothers knew the later revelations from the beginning.
For an expanded story, you are meant to watch the Animatrix in between One and Two, especially Final Flight Of The Osiris, and play the Enter The Matrix game.
