Anakins Doubt

In the prequels that we have Anakin turns to the dark side because he can't accept that people he love might die... WTF! I mean the jedi have many customs that the story could have focused on. The fact that they take infant's from their family's is one. The fact that they are not allowed to marry, or that they claim to be above politics and don't take sides they still fight for the republic.
The one I would like Anakin to be most conflicted about would be the practice that jedi should be separated from their family. Something he was until the events of Episode 1 where he finds himself meeting his mother and father. Whom is non-other then Qui-Gon Jinn. In this version Qui-Gon is a ex-jedi whom was kicked out of the order for trying to stop it from taking his son away from him. Something that imprints the idea that the jedi are far from perfect in Anakins mind, which is something that changes his view of the universe.

Consequent Changes

The main change is that Anakin will start to doubt the jedi and their practices. Questioning the jedis influence over the republic senat and armed forces. He will also start to question the jedis claim to fully know the nature of the Force. Wondering if the dark side is truly evil or if the jedi are just blinded by doctrine.
Through out the three films, and the Clone War series, Anakin find himself in situations where the use of the dark side have "good" consequences. Where his rage, saves the life's of countless lifeforms. Where his trickery wins him battles. And when his feelings for Padmé keeps him from doing horribel things, like leaving people in suffering just because he can't save them next time.
This doubts will be something that Palpatine will use to slowly take control over Anakin. In part by not striking first at the jedi. Instead claiming that all he did, he did for the Republic. Even going so far as manipulate Anakin to believe that the true enemy Dooku, tried to grab power because of he still holding on to a number of false jedi beliefs.