Anakin was always the Chosen One, but the Jedi were too arrogant to realize the will of the Force. In order to bring "Balance" to the Force , BOTH the Jedi and Sith had to be "rebooted" if you will, for Luke to establish the New Order of the Jedi.
Anakin was the Chosen one who was doing the will of the Force and NOT whatever path the Jedi Order "thought" he should be following to achieve his goals as the Chosen one.
By AOTC, the Jedi Order had reached their apex of arrogance and had engulfed themselves into running a major intergalactic War. If you remember, in TPM ,Qui-Gon Jinn told the Queen that they could protect her, but not fight a war for her. Qui-Gon was more in tune with the Force , than perhaps other Jedi of his day. Qui-Gon knew the score, if you will, eventually he became Master to his Master!
Anyway that's the way I always saw the whole Chosen one question, and in regards of Mace vs. Palpatine, it doesn't really matter who was beating who , because eventually it was the will of the Force that Palpatine walk out of that office alive. The Irony of it all was that as much as everyone had been a pawn to the Emperor's plans, no one was a bigger pawn than himself, despite all of his hatred for the Jedi, he was one of the major role players in the re-establishment of a new Jedi Order!