There's actually something rather brilliant there that I think George did: He made it understandable why Anakin distrusts the Jedi. Though they represent all that is good in the galaxy, they scheme and plot, bicker, become angry, sad, and emotionally involved. All the things they aren't supposed to do. This is why the force needed to be balanced. This is also why the Jedi didn't really understand what balancing the force really meant. It meant, basically, that there needed to be a blank slate so they can start over.

Vader cleansed the galaxy of the Jedi and defeated the only Sith, removing himself as the only remaining Sith in the process. So in the end, we're left with one genuinely good soul, one man that can uphold everything the Jedi are meant to uphold: Luke Skywalker. And the Force is balanced.

Lucas told that very successfully, and to me that is why the prequels will never be a failure in my eyes. Failure at certain things? Absolutely. But a complete waste? Far from it.