I prefer the droid factory scene over the deleted scene “Dooku interrogates Padmé.” In the deleted scene, Dooku offers clemency if Naboo joins the separatists. But Padmé could no more withdraw Naboo from the Republic than a U.S. Senator could withdraw his State from the Union. Surely only the Queen could secede. The droid factory scene - or an alternate capture scene - is crucial to the plot. It explains why Anakin only wields a lightsaber in the arena once the Jedi arrive. Without it, Anakin and Padmé seem to willingly walk to their deaths.
Actually, that part really does bother me, now that I think of it. I understand why he removed the droid factory scene, but the scene he replaced it with just feels so abrupt and awkward. It’s like “Hey, let’s go talk with Dooku” skip to suddenly at the table with Dooku “Oh hey that didn’t work, guess we’re gonna die”.