I really hope they don't make a new protagonist. Nathan Drake IS Uncharted to me. Replacing him would be like going to an Indiana Jones movie and having Sallah be the central character; it could be awesome but it wouldn't be Indiana Jones. If they want to make a new protagonist more power to them, just call it something else.
As some other people said earlier Sovereign. No villain or character in a video game has given me chills like I got during this conversation. Sovereign just comes off as so alien, uncaring, and superior that it sets up the reapers to be these horrifying lovecraftian monsters. Of course, the Reapers ended up being ruined by the subsequent games, but Sovereign remained creepy and unsettling even after that. Maybe it is because Harbinger and the other Reapers spend so much time going after you directly and Sovereign only really makes a move against you once. He thinks of himself as so high above you that you're never really considered a threat to him at all just a threat to his pawns and you honestly feel like that's true because you only barely manage to defeat him in the end. It's a shame that none of the other Reapers could live up to him.
Also I second Andrew Ryan and GLADOS. They're much better villains than Sovereign, but I feel other people could write about them better than I could.
Justin, please please please don't do anything stupid! You have an entire community here for you and whatever is upsetting you isn't worth doing this for! Just talk to us and tell us what's wrong, or really just talk about anything. Just don't do this man!