I agree that the Jedi should have had faults in the PT. The OT made Yoda and Obi-wan look like real dipsticks, and that should have been reflected in the PT. But that could've been done without retconning the Jedi into an insular cult. It would have been enough to say that the Jedi are so busy fighting the Clone Wars that they don't notice this guy is starting to crack under pressure, adopting unorthodox methods, reading forbidden scrolls, and all that.

In a way, it's too bad that Lucas had so little to do with Star Wars from 1983 until 1997. The story of an strictly monastic Jedi cult that drives one of their members to the Sith is a pretty good one, and he could've given the story germ to an EU writer to flesh out. It could have been one of the Tales of the Jedi stories, thousands of years before ANH. It's a good story, it just doesn't work as Anakin's story.