I've been considering my own Prequel rewrite ideas for a while now (inspired by various ideas from this site as well as others), and one of the big areas of debate seems to be that if the reveal in ESB is to be kept secret, how can Anakin's fall also be shown in a prequel film.
My way of tackling this was going to be have Obi Wan and Anakin meet in Episode 1 (or shortly before it) where they become good friends. Obi Wan begins teaching Anakin towards the end of this film. Then by the start of Episode 2 Anakin is already showing much promise as a Jedi, however, he does seem to be less true and noble than Obi Wan, and it seems that Obi Wan has to keep him in line so as not to stray to the Dark Side. Then as the movie goes on Anakin is away from Obi Wan, and when the two are next reunited Anakin does seem to have developed some bad ideas and have slipped a little, but Obi Wan manages to convince Anakin to do the right thing and go help fight the new bad guy (Darth Vader). The bad guy wears a Vader style outfit (Vader-lite if you will), but no helmet. This style of costume however, is worn by many of the Jedi as their battle armour, and Anakin's and even Obi Wan's clothing is not massively different.
Then the audience would only see clips of the fight (because Obi Wan would be off fighting someone elsewhere and it would be cutting between the two scenes). We would see the two prepare for battle, perhaps casting their cloaks to the floor, Anakin wound Vader's face, Vader seeming to get the upper hand, both dropping their lightsabers during the struggle, and then Obi Wan appraoching so only from a distance we see the characters fighting near an edge, neither still holding a Lightsaber, and one falling to their death (in a way in which the body cannot be found, lava perhaps). Obi Wan shouts 'No!', then before he can arrive we see the surviving character pick up a cloak from a dead soldier nearby, wipe his face and we see the blood on his arm, so he wraps the cloak around his face, then a helmet from a nearby guard he killed earlier is lying there. He picks it up and puts it on, then he picks up the two lightsabers, throws Anakin's asside and leaves. Obi Wan then arrives to find Anakin's lightsaber, and is clearly upset. He gives the news to the others that Anakin has been killed by Darth Vader.
As long as there was a scene or two before this where we see this Vader character killing other jedi, and those scenes were only shown in brief clips, it could be done because the audience doesn't know the name of this character and that would seem like it is his identity being kept secret, Anakin could be shown elsewhere during these murders so that he isn't a suspect.
Then to solve the Obi Wan/Anakin fight, it would be that Obi Wan fights the new Vader (who is actually Anakin), where he could seem to be angry with him, and we assume it is because he killed Anakin, whereas really it is because it is Anakin, just like we assumed when he saw someone fall off the cliff and die Obi Wan shouted NO because it was Anakin, when really he just didn't want Anakin to kill someone (this interpretation would vary depending on how early you wanted Obi Wan to know Vader was Anakin). Then when they fight Obi Wan 'defeats' Vader and leaves. Then Vader is repaired and the rest is still in tact. After this point I don't think there would be many people left for Obi Wan to have to inform about the true identity of Vader, and the lie he tells Luke could be the one he had originally told people after he initially thought Anakin was dead.
I think we are possibly overthinking this because the whole idea is to make it so first time viewers are shocked by the fact Vader is Luke's father. I think this way it would be quite shocking, the only reason we don't think it is shocking enough is because we already know the outcome.