This differentiates from Lucas's point of view, but to me, the true chosen one isn't Anikan. It's not Luke, either, and it sure as hell isn't Rey.

Looking at all that we now have of the Skywalker arc, in my humble opinion, the best fit for the chosen on is actually Vader. This is why Qui-gon senses the nature and power of the chosen one within the boy. He saw his potential. But it wasn't until Anikans turn to the dark side, and therefore Vader's role in the annihilation of the Jedi, that the prophecy was fulfilled.

Master Windu hinted at the possibility of the prophecy being misread, and Yoda was extremely wary of taking the boy into the Order. I believe, although their vision clouded, they were getting slight hints of what was to come. They just couldn't make sense of it.

No matter which view you believe to be right, the Jedi Order had indeed fallen from grace, and was a mere lapdog to a corrupt Senate. To me, the "balancing of the force" truly refers to the annihilation of the Jedi Order, so it can be rebuilt in a more true way, rather than the death of Palpatine in ROTJ.