I think Anakin is going to kill Count Dooku in Ep3 as a test to complete his tranformation to the dark side. Just like how Palpatine wanted Luke to kill his own father and turn to the darkside.

I really did like Count Dooku in AOTC, but I hated that lightsaber duel with Yoda. That was just stupid! The choreography doesnt even make any sense when Yoda is jumping around like a monkey and Count Dooku is just swinging his saber over his head like he's fighting an imaginary character. There's one instance that makes me cringe, and that's when Yoda jumps on a rock behind and above count dooku's head. Why didn't Yoda just cut his head off while he was up there instead of jumping around? Poor work on behalf of the animators.