It's not the takes that were wrong (most were probably the best takes available). It's not the CG that was wrong (some shots were done well). It's not the line readings that were wrong (they mostly did a reasonable job with the material). It's not even the plot that was wrong (A political drama of galactic scale is inherently cool).
It's the philosophy that was wrong.
Truth is always found in Pure, Beautiful Simplicity. It doesn't matter if the surface of the movies looks good or not, it's the soul of the movies, the story, that matters. Luke had a goal (become a Jedi). He worked toward that goal (trained with Yoda). He found himself unable to continue (Vader was his father). He overcame this obstacle (redeemed Anakin Skywalker and became a Jedi).
In short, Luke had a worthy goal, and overcame his weaknesses to achieve it.
Anakin has several goals:
1. Explore all the stars in the universe.
2. Become a Jedi.
3. Return to Tatooine and free the slaves.
4. In particular, free his mother from slavery.
Right of the bat, his motives aren't very clear. He wants to leave, but he also wants to return, for example. Furthermore, he never achieves any of these goals except #2, and that happens somewhere off screen in between movies. Even then, he doesn't truly become a Jedi, as he is married to Padme in violation of the Jedi Code. By Episode 3, his original goals are irrelevant. It's difficult to care about a character who casts aside his own goals so lightly.
The original trilogy works because we can believe that Anakin Skywalker was once a good man. In the prequels, I can't imagine that Anakin was ever a good man.