The only real interesting way to change the Dooku character into something meaningful is to have him mean something in the overall story or better yet in Anakin's specific story arc (otherwise its just changing him for the sake of changing him)......if Anakin killed him, but then it was discovered that Dooku WAS in fact just a "grey area" jedi...neither good nor bad....and that he HAD discovered that something was up and was maybe trying to do something about it from the inside (which meant letting the rest of the Jedi believe he had turned to the dark side)......it makes Anakin's killing of him a bit awkward........AND then you can show Anakin struggling with the fact that he ENJOYED killing him (lending itself more appropriately to the idea that Anakin was SEDUCED by the dark side, and not tricked by Palps).

But, as it has been said many times, short of a reshoot of the entire film....much of this cannot be achieved.