The prophecy was that a "chosen one" would bring back balance to the force. In the prequel trilogies, the light side and the Jedi dominated the force. It was Anakin's rise on the dark side that brought destruction to the Jedi order and balanced things back out from all light to light and dark (hence the name of episode three.... "Return of the Sith").
Remember, Yoda said in "Attack of the Clones" that "Misread this prophecy may have been". For some reason, the Jedi thought that the prophecy meant that some 'chosen one' was going to lead them to some special golden age, when in fact, it meant an actual re-balancing of the force with the emergence of the Sith again.
I think that is what the whole 'prophecy' storyline was about.