Obi-Wan described Anakin as a Mary Sue to Luke, in the context of lying like a rug about everything else.
So I think that tale could have been finessed into "Anakin was a great Jedi, a courageous warrior, charismatic as hell and a wonderful friend, but with the fatal flaw of hubris that none of us really saw until it was too late, including your mother. But hey at least he wasn't an annoying whiny little bitch like his son."
I'm okay with what they're doing with the story in
The Clone Wars, but I still think the best way to do the story would have been to give Anakin a fatal flaw that could explain his entire fall, yet not render him contemptable or annoying beforehand.
He should have been a perfect golden boy, except for a tendency to believe his own press releases about being The Chosen One. Arrogance can be kind of charming in an otherwise charismatic, intelligent, sensitive and moral guy; power hungriness might just be a healthy degree of ambition.
There was never any need for the character to be some annoyingly perfect Mary Sue, and in fact, that wouldn't have made any sense.