Was Anakin actually the Chosen one?
Let's examine the facts. First there is the mysterious prophecy of the one who will be conceived by midi-chlorians and bring balance to the Force. Anakin does seem to fit this bill according to Shmi's testimony and in addition he has the highest midi-chlorian count of all the Jedi that ever were or ever will be. However, what exactly does "bringing balance to the Force" mean? It was suggested once to me that in turning to the dark side Anakin was fulfilling the prophecy, because wouldn't bringing balance to the Force mean balancing light and dark and having a constant presence of both? However, the Jedi definitely connect bringing balance to the Force with destroying the Sith. My interpretation of balance is that the Sith are an imperfection, a heavy blight upon the galaxy, and removing them will lift that burden and restore balance (think of a set of scales). Or it could be interpreted as stability and as we all know, the Sith are far from stable, acting upon passion instead of reason.
If Yoda was correct and the prophecy had been misread, well then quite frankly, it could have said anything, but where exactly did this prophecy come from? I think that is quite an important piece of information. Who made the prophecy and when? How common are prophecies anyway? At any rate, the prophecy must have been made thousands of years before Anakin was born. There must have been other prophecies and ones that were fulfilled for the Jedi to give merit to this one, but as to where the prophecies come from may always be a mystery.
Although, Anakin falls to the dark side he does in the end kill the Emperor and turn back to the light before he dies. However, Luke's contribution to these events cannot be ignored. I would argue that Luke might, in fact, be the Chosen One or at least the one to bring balance to the Force (which could lead to a discussion about who is more powerful: Luke or Anakin, but I won't get into that right now). Of course, the Star Wars novels have invented new Sith, post the deaths of the emperor and Vader, for our heroes to face, and if these are taken into account, then probably neither Anakin nor Luke are the Chosen One. However, I think of the novels as merely being fiction about fiction and should not necessarily be taken at face value, unless Anakin is the Chosen One even though he himself does not destroy the Sith but his offspring does. That is one way to look at it and it gives the Skywalkers a chance to fight Sith Lords for generations.
However as I value the movies far more than the books, I do think that Qui-Gon was right. All signs point to Anakin and perhaps his fall to the dark side and the atrocities that he committed are not as important as the fact that he did in the end destroy all the Sith.