Again, i'm not saying they didn't plan to make a trilogy out of The Matrix, what i'm saying is they didn't know how the other two movies would play out until they started writing them. They had a basic idea of which direction they would go, the obvious showdown with Smith, Neo facing down the machines and so on, but the detail and tying all the plot lines together only happened as they wrote it.
For some reason the link i gave above is redirecting somewhere else. It was a link to an actual draft of the script.
Try this link. It has a link to the actual PDF that the Wachowski's wrote the script on, and it is dated October 2001. That's two years after The Matrix was released, and it was still only in draft then. Think about it, if it was already written in 1999, then why was it not released until 2003? It's because parts 2&3 spent a year in pre-production (2000-2001) they took a year to shoot (2001-2002) and a year in post-production (2002-2003). Reloaded and Revolutions were produced and shot back to back.