At the conclusion of the duel between Obi-Wan Kenobi and the newly christened Darth Vader in Episode III: Revenge of the Sith, after Kenobi had proven to be victorious, Kenobi had this to say to a a writhing Vader:
You were the Chosen One! You were supposed to destroy the Sith, not join them! Bring balance to the Force, not leave it in darkness!
According to the words spoken by Kenobi, one might be led to believe that the prophesy had not been fulfilled, but upon closer inspection, one should conclude otherwise. At the time of Episode I: The Phantom Menace, only the most ardent of Sith devotees could claim that the Force was in any way balanced, at least from the perspective of Dark side strength versus Light side strength in the galaxy.
There was a reason that Episode I was titled as it was. The Sith menace to the galaxy was something that was largely hidden. It was the phantom menace after all. On the other hand, the Jedi were thriving. The Jedi had a veritable who's who on their Jedi Council. There was Master Yoda, Master Mace Windu, Master Adi Gallia, and, dare I say it, Master Saesee Tiin! In addition to this murderers' row of Jedi Masters (oh, and you better believe there were more than just these few that I've named!), there were a host of Jedi Knights, Jedi Padawans, and even some Jedi Younglings (a younger class of Padawans). And then of course, the Jedi had their swanky Jedi Temple and Jedi Council chambers on Coruscant. The Sith were essentially thought to be extinct by the Jedi at this point in time.
As powerful as Darth Sidious would prove to be by the end of Episode III, and as skilled as Darth Maul was in showing his ability to simultaneously take on Qui-Gon Jinn and Kenobi in Episode I, there is no way that this Sith duo could have prevailed in an open conflict versus all of the Jedi. Even in Episodes II and III when the more powerful Darth Tyranus joins Sidious, the two would not have been a legitimate match for the Jedi. It is only in weeding out the Jedi numbers that one can make the claim that the force is in balance: the Dark side is as strong as the Light side.
Anakin Skywalker, in becoming Darth Vader, helped this to come about. By intervening as Master Windu was on the verge of killing Lord Sidious, by leading an army of clones into the Jedi Temple to defeat Jedi that might be within, and with the assistance of Order 66, Skywalker/Vader did bring balance to the Force. Was there ever a greater balance between the Light side of the Force and the Dark side than there was during the juxtaposed climactic duel between Kenobi and Vader and the climactic duel between Yoda and Sidious? In watching the duels, if you did not know for a fact how the story had to end, you could envision either duel resulting in either combatant winning.
As for the other part of the prophesy, Skywalker did eventually aid in the destruction of the Sith. It is true that his part in the destruction of the Sith only occurred after he had joined their numbers, but in turning from his master and going to the aid of his son in Episode VI, Anakin Skywalker did finally complete the fulfillment of the prophesy that he would destroy the Sith and that he would bring balance to the Force, if not in that proper order.