Unlike the other villains, Rafe had a personality that stood out the most. He was charming, sarcastic, cunning, and even comedic at times. This intrigued me about Rafe over the other villains, because he shared many of those character traits with Nathan Drake, himself.
On top of everything else, his boss fight was by far the most challenging. You actually had to be careful and watch his movements, while the other boss fights were mostly run and gun or constant punching. It was a true challenge and the most memorable of boss fights.
These are the reasons why I think Rafe is the best Uncharted villain. If there is indeed a potential sequel, I believe it would be hard to top off Rafe.
