No matter what you believe the Prophecy means, Anakin is the Chosen One, so he has to be at the center of fulfilling it. And Anakin isn't at the center of wiping out the Jedi. It was just through skill and luck that Yoda and Obi-Wan survived, and if their survival is necessary for balance, Anakin deserves no credit there. Let us also not forget that Order 66 was carried out across the galaxy, not just on Coruscant. It was the stormtroopers who did most of the work on that count, both on Coruscant and elsewhere. Secondly, no one has been able to give me a viable explanation as to why Anakin would be destined to only be the apprentice to the real architect of the Stih plan. Palpatine is the one who set the plot into motion, Anakin is nothing more than a pawn, and the very last pawn used at that. Palpatine got where he was with a lot more help than just Anakin's. Why would it be his Force-dictated destiny not to be the one who brings the Sith to power, but to be that person's attack dog. If that's what the prophecy means, Palpatine would be the Chosen One, and he isn't. Plus, there would be no need for the Rebellion that would ultimately overthrow Palpatine. If the Force wanted him in power, then it is Luke, Leia, and their contemporaries who are truly contrary to the will of the Force.