1. Note how utterly derailed this thread has become. Discussion of screenwriters transformed into an argument about whether a corrupt Sith politician is a better villain then an insane pink teddy bear.
2. They were both well written villains. Toy Story 3 was an enjoyable, family-oriented, animated film. Star Wars is an enjoyable, epic space saga filled with Lightsaber-wielding warriors and politicians with Force Lightning*. Comparing the two is like comparing an apple and an orange. It isn't which is better, it's which you enjoy more.
On a side note, it is ironic: Pretty sure that neither Disney/Pixar OR Lucasfilms planned on a second film**.
*: Referring to SW as the Films, not the Films+EU. Toy Story doesn't have any backgrounds like the EU that Star Wars does. Quite frankly, I know of a lot of people who would gladly forfeit the EU of Star Wars and have the Force be as mysterious as the reason for why the Toys are alive. These are not my personal views, however.
**: Technically, Lucas DID have a backup plan: If the first Star Wars movie failed (ROFL) he had a sequel written to try and revive it. The sequel evolved into a book whose name escapes me.
Good point. They really are apples and oranges.