Sunrider101

I think one of the most important things to consider when attempting to keep Vader's identity secret is that in order to mislead the audience, they must believe Obi-Wan's story in Episode IV.
"A young Jedi named Darth Vader, who was a pupil of mine until he turned to evil, helped the Empire hunt down and destroy the Jedi Knights. He betrayed and murdered your father."
After all, if Obi-Wan is known to be lying (there is no second apprentice, or the second apprentice does not appear to kill Anakin) it would be far too easy for the audience to simply connect the dots and guess it was Anakin.
I think the best way to do this is to have (similar to Duracell's idea) a second apprentice of Obi-Wan's throughout the prequel trilogy.
However, I think the apprentice  should be the main antagonist (replacing the roles of Maul, Dooku and Grievous.) (I like to call him Xanatos as a throwback to the Jedi Apprentice novels that featured a character of similar description.)
Obi-Wan would be attempting to redeem his former apprentice as he also attempts to train Anakin. Anakin and the apprentice would grow to hate each other over the course of the clone wars and eventually it would culminate with a final battle between the two where they both are severely injured (fall off the platform and burn perhaps).