This question could be rephrased as: when making the PT and overseeing the design of the Separatist ships/droids/vehicles etc., why didn't Lucas design them in such a way that they could be perceived as evolving into a lot of OT things later, like he did with the Republic hardware. Here's one possible, quick answer that I don't think is satisfactory. Although Palpatine/Sidious was the ultimate leader of both the Confederacy and the Republic, he took the former less seriously and that it was always going to be the Republic, and therefore its associated hardware, that was going to become his Empire. I have a couple of problems with this. Firstly, As Lucas himself said, in TPM, he was carefully monitoring the effectiveness of the droid army with a view to its potential future uses. It was only when he saw its shortcomings (central control, no independent though or creativity) that he ordered the Clone army. So Palpatine was not, in principle, against taking aspects of the Separatist war machine seriously as forming part of his future military apparatus, he just saw that the droids were very limited. He could still have made later use of, e.g. Separatist ships. Secondly, it seems to me that, post Ep.III, the Separatist forces, although having been disbanded, neverthless left behind a huge military apparatus. Irrespective of the fact that Palpatine was also behind the Confederacy, the fact is, this vast armada of ships, droid weapons, etc. ended up being entirely at Palpatine's disposal, and he could make any excuse he liked if he wanted to incorporate it into the Imperial Armed Forces. So, why didn't he? I can understand him wanting to bin the bog-standard battle droids, but I'm sure he'd be able to find a use for the droidekas. DL EDIT: In fact, I suppose the Death Star itself is an example of Separatist technology that ended up serving the Empire, but there aren't many others.