At the time of the 1st film the brothers stated quite clearly it was part of a trilogy. Reloaded and Revolutions were always two films and it was Joel Silver, around this time last year, who described them as one big film cut in half. Having seen both it is quite clear that they are two different films, the end of reloaded removes the 'security' of the prophecy from the main characters and they respond accordingly in Revolutions.
From the moment it became clear that the Matrix was a success and Warners greenlit the sequels, they were submitted as two films, written as two films, produced as two films and marketed as two films. They were, however, filmed together. Kill Bill was split into two quite late into the production and editing process.