The more I think about it, this is another case of being misled or lied to before we see the movie to keep some surprise left in it.
Dooku is Anakin's Dad period.
Empire Strikes Back: "I am your father."
Luke: "Ben, why didn't you tell me?!"
ROTJ: Palpatine: "Now fulfill your destiny and take your father's place at my side."
Revenge of the Sith
Palpatine: "I'm sorry Anakin, but the late Count Dooku was your father."
Anakin: "Mace! Why didn't you tell me?!"
Palpatine: "Now fulfill your destiny and take your father's place at my side.
Palpatine's seen this all before. That's exactly why he's so overconfident about Luke turning to the Dark Side in ROTJ.
They have pickup shots they've been doing, and when they made ESB, it was very closely guarded and David Prowse didn't even know until he saw the movie.
In ROTJ, the scenes with Vader unmasked - again, almost no one knew. 4-5 people comprised the whole crew including Hamill and Shaw when the final scene was made.
Mark my words:
1) Dooku is Anakin's father and Anakin kills him without ever knowing and when he finds out the Jedi lied to him, it throws him over the edge. It's the only obvious way for the story to proceed.
2) Han Solo is a new kind of Clone Trooper who's programming as a child was interrupted, causing him to develop personality, morals, and independence "he's Solo."
Do this: Watch Episode 1 and assume two things:
1) Shmi Skywalker is lying about Anakin's father. How does she act when observing Qui-Gon's curiousity about her child? If she'd known Dooku 9 years ago, wouldn't she have already heard of Qui-Gon Jinn, even if she'd never met him? Could that have helped her decide to let Anakin go with him?
2) the midichlorian blood test results will become known to Mace and Yoda that Anakin is Dooku's child by some point before the Theed Celebration (doesn't really affect TPM movie, but plays a part in E3).
Watch Episodes 4,5 and 6.
1) Assume Han Solo is a Clone - the kind used for classic Stormtroopers.
2) Recollect that Boba Fett is an obsolete Clone - the Mandalorian kind killed off and replaced by other types during the Clone Wars.
3) Consider Boba's pride in his father. What would he think of the new Stormtroopers, and especially a Rebel and criminal like Han Solo?
Come back and tell me how you felt characters responded and acted during the movies if you considered these things were going on.