The reason why there seem to be loopholes in the character of Dooku is that George Lucas came up late in the writing process with this new character.
The original plan was to have Sidious has the one who ordered the clone army but was later change to Dooku since Lucas needed a new villain to fight the Jedis at the end.
More importantly, the whole description about Dooku that was part of the second script of Attack of the Clones was taken out. It explained why he turned that way, who ordered the clones and what happened to those missing files in the archives.
A major event in the screenwriting of Episode II was the creation of the new Sith apprentice, Count Dooku, also known as Darth Tyranus. For such a major player in the last two episodes, Dooku was invented considerably late in the game, during the pre-production period of Episode II. Lucas’ outline for Episode II must have been merely that Sidious somehow fosters a Separatist movement, possibly by manipulating a powerful politician to lead the faction; at the same time, Sidious has found a new Sith apprentice, who duels Yoda and Anakin at the end of the movie, and in the subsequent film Anakin could finally slay the apprentice and take his place as his final act towards the darkside (this would inevitably be re-structured, as we will later see). The new Sith apprentice was at first thought to be similar to Darth Maul in the previous film, powerful and menacing, but whom served little plot use other than to provide a threat and duel the heroes at the film’s conclusion. Likely, the new apprentice was to oversee the Separatist leader, similar to the way Maul protected and kept an eye on Nute Gunray and the Neimoidians in Episode I. The art department went back to some unused designs from Episode I, namely the popular “Sith Witch” design, which would eventually find its way into the Clone War cartoon series as Asajj Ventress. At one point Lucas suggested a robot-cyborg, indicating he was interested in the concept that would eventually become General Grievous in the following film.
However, Lucas soon drastically changed his plan, offering concept artists the idea that the new Sith would be a completely different character played by Christopher Lee—the apprentice could be the opposite of the fearsome and acrobatic Maul, instead a thinking man, older and with a sense of elegance and regality. Whether before or after this happened, it seems Lucas struck upon a much more interesting direction to take things—the Separatist leader and the Sith apprentice would be the same person. And thus was born Count Dooku, also known as Darth Tyranus. Once again we see a similar situation and process which led to the merging of Father Skywalker and Darth Vader in 1978, or to the merging of General Darth Vader and Prince Valorum in 1974, as character and story redundancies are simplified.
In Dooku Lucas created one of the prequels’ most fascinating characters. An elderly Jedi knight who left the order after becoming disillusioned with the Republic, he is picked up by Sidious, who tells him of his plans to create a New Order and thus rid the Republic of its corruption. Dooku secretly joins the Sith, becoming Darth Tyranus, and creates the Separatist movement. Later, during pick- up shooting, Lucas would write that he was also Qui Gon’s master (probably an inspiration taken from a scene in which Jocasta Nu compares the two), adding further complexity and perhaps linking Qui Gon’s outsider tendencies as a trait picked up from Dooku, creating an interesting relationship between Dooku and Obi Wan and Anakin.
In effect, Lucas combined Palpatine and Anakin into a new character—a Jedi who becomes a Sith while also being a political figure and master manipulator with a secret identity. Lucas also developed an interesting history that would be cut out of the final film, that of the “Lost Twenty.” The scene is portrayed in the shooting script:
INT. JEDI TEMPLE, ARCHIVES LIBRARY - DAY A bronze bust of Count Dooku,
stands among a line of other busts of Jedi in the Archive Room. [...]
OBI-WAN studies the bust for a few moments before MADAME JOCASTA NU,
the Jedi Archivist is standing next to him. She is an elderly,
frail-looking human Jedi. Tough as old boots and smart as a whip.
JOCASTA NU Did you call for assistance?
OBI-WAN (distracted in thought) Yes... yes, I did...
JOCASTA NU He has a powerful face, doesn't he? He was one of the most
brilliant Jedi I have had the privilege of knowing.
OBI-WAN I never understood why he quit. Only twenty Jedi have ever
left the Order.
JOCASTA NU (sighs) The Lost Twenty... and Count Dooku was the most
recent and the most painful. No one likes to talk about it. His
leaving was a great loss to the Order.
OBI-WAN What happened?
JOCASTA NU Well, one might say, he was always a bit out of step with
the decisions of the Council... much like your old Master, Qui-Gon
OBI-WAN (surprised) Really?
JOCASTA NU Oh, yes. They were alike in many ways. Very individual
JOCASTA NU stares at the bust
(continuing He was always striving to become a more powerful Jedi. He
wanted to be the best. With a lightsaber, in the old style of fencing,
he had no match. His knowledge of the Force was... unique. In the end,
I think he left because he lost faith in the Republic. He believed
that politics were corrupt, and he felt the Jedi betrayed themselves
by serving the politicians. He always had very high expectations of
government. He disappeared for nine or ten years, then he just showed
up recently as the head of the separatist movement.
As is evident, the development of Count Dooku was an organic and unplanned process, and his central role and highly developed characterization were entirely serendipitous. As quickly as Dooku was developed, however, he would also be eliminated.