I think he should've become Vader earlier. Episode 1 should've started with Obi Wan discovering Anakin as some rough around the edges ace pilot with promise. Maybe the impending Clone Wars has caused the Jedi to search out anybody who looks like they might have a knack for combat.
Show Anakin as more of what Luke might've been if he hadn't been held back by Owen. Maybe Anakin feels he's stuck in life, and sees Obi Wan as a chance for "Adventure, and excitement" like Yoda sensed in Luke.
Maybe have them grow close in their early adventures. Then the second film starts with the shit hitting the fan, and have it take it's toll on our heroes, and begin to create a rift between them. Then go with the standard Palpatine whispers in Anakin's ear, and makes him think that Obi Wan is a doo doo head. Instead of a blatant enemy, such as the sith with the red sabers. Maybe there never was such a thing, and Anakin blindly follows Palpatine much like many people followed Napoleon or Hitler, and he truly believes he is a good man. Heck, maybe have everybody know that Palpatine is a jedi. After all, the Jedi are entangled in politics. Law enforcement officers end up politicians quite often. Shove in Anakin in love story for good measure.
I think the promise that Palpatine is a going to be a great leader during the hard times the Clone Wars have brought forth is good for his uprising. Anakin's slip to the dark side could've been less drastic and more gradual. One thing I've noticed with great villains, is the fact that many of them believe what they are doing is right.
Obi Wan and Anakin could have their duel at the end of episode II, and end it with Anakin's supposed death. Episode III would start with many dark jedi, including Darth Vader, attacking the order, which would've already been weakened by the clone wars. You could have a duel between Vader and Obi Wan, lacking a lot of dialogue. I think the two being angry at one another is enough for consistency without giving away the identity.
There's more you could build off that basic outline..