Omg. I can't believe they had created all that, then actually thought making the changes to give us Fate/Stay Night was a good idea. It's like, how in the world did something so awesome (Prototype) become so bad (Stay Night)?
About the only thing I'd say was an actual improvement over Prototype was Gilgamesh, and since we didn't get to see any real characterization in a 12 minute short, who knows...maybe he was even cooler as envisioned in Prototype, and they just didn't show any of it.