In Episode II, Anakin and Obi-Wan, and eventually the Yoder himself face off against Dooku. Dooku's ship is right there. He's not even that close to it! It's obvious that Dooku wanted to escape. He came to a hangar, which has a ship in it, and a pilot droid just got into it. So why didn't one of the three just run over real quick and trash the whole insides! Just 2-3 swipes of a lightsaber and the pilot droid is gone, and basically everything else that is necessary for flight could be damaged...even the windshield. Now Dooku doesn't have a way off of Geonosis. His only option is to battle the 3 Jedi and win. In Ep. II, Dooku's fighting the Yoder and he senses that he can't win so he jumps aboard his special ship and flies away. But if there's no special ship for Dooku to get into...he's kinda screwed.