In general, a story like the Prequels is very hard to write. A “good guy turns evil” script is not easy to pull off in a believable way, especially in only 3 movies. Yeah, the Godfather pulled it off, but that’s why its revered as a classic. Also, Michael Corleone went from a normal every-man to a very unforgiving mafia boss. Anakin has to go from an honorable, likable hero, to a genocidal fascist cyborg in only 3 films. This kind of story is hard to pull off, and I almost wonder if The Phantom Menace was Lucas’ way of unconsciously procrastinating on all that difficult dramatic writing.
Anyway, I think the best way to implement Anakin’s fall is to tie it in with his experiences in the Clone Wars. Anakin constantly sees his fellow soldiers die as the Republic takes losses, but the Republic and the Jedi insist on maintaining high moral standards during warfare. Meanwhile, the other side regularly commits war crimes. At some point, in desperation, Anakin begins indulging the Dark Side by doing something like force choking a prisoner during an interrogation. Things just escalate from there. A turning point could be when Anakin defeats a major antagonist in a lightsaber battle by fully embracing the Dark Side in a moment of rage/desperation (like when Luke flips out at Vader), except Anakin just kills his opponent in cold blood after they surrender. Anakin begins to rely on the Dark Side more and more, realizing how powerful a thing anger can be. Obviously, Palpatine takes notice and begins to encourage this. By Episode 3, Anakin is regularly running clandestine missions for Palpatine where he often assassinates people. But at this point we can still consider Anakin more of an “anti-hero” than an actual villain, since he’s mostly only killing bad guys… for now.
I think it would be cool if Episode 3 opened up with a sequence that sort of contrasts with the beginning of Episode 6. In Episode 6, Luke does everything he can to try and peacefully resolve the situation with Jabba, turning to violence only when Jabba leaves him absolutely no other choice. In Episode 3 we could have a contrast, where Anakin has to resolve a problem with some third-tier villain. But instead of attempting to bargain and resolve things peacefully like Luke, Anakin just shows up and murders everyone.
Episode 3 needs some climactic event that really pushes Anakin over the edge. I think it would need to be something like Padme dying - perhaps in a way that causes Anakin to blame the Jedi for her death. (Maybe she dies during an attack on Coruscant, and Anakin resents that the Jedi were too devoted to their peaceful philosophy to effectively protect the populace.) Anakin starts to believe the Jedi don’t really understand the Force, and sees their fear of the Dark Side as foolish and narrow-minded. Eventually, the Jedi realize Palpatine is a secret Sith, and they attempt a coup, which Anakin thwarts. We can then have Anakin lead the assault on the Jedi temple, and eventually, confront Obi Wan (who really needs to be setup as Anakin’s closest friend/mentor early on in Episode 1).
Anyway, I think that’s the best way to write this. No need for weird prophecies or fun with Darth Plagueis or whatever. Just a slowly escalating addiction to power and control, that begins with desperation and fear brought out through war, and culminates in total megalomania.