I would prefer to see Dooku appear watching Qui-Gon’s funeral from a distance as a sign of his disaffection with with order. I don’t want him to be Sith at all but a Jedi who has correctly detected the Sith infiltration of the Republic and is trying to do something about it. It gives his character more depth and allows Palpatine to use the war as a propaganda tool against the Jedi no matter who wins.
He was a prime example of how much dark side can corrupt. (and the movie would be really dull if you eliminate him as the enemy) You know, actually you can have it both ways. We know that he joined the sith as he was Darth Sidious’s apprentice, but why did he exactly do that? Perhaps by joining the sith and raising the drone army, he was trying to prove something, at least at first. Realizing he couldn’t convince Jedi to take action, he would force their hand before it was too late. But he was corrupted by the dark side before that. (he was already on his way to the dark side, what he did with good intentions was what tipped the scales)
So he took a sith apprentice and joined forces with Darth Sidious to teach the Jedi a lesson, but was betrayed by the latter. Or something like that.
Prequels already quite weak as it is, reducing the number of sith wouldn’t help the matters.