I would prefer the new protagonist to be a lone wolf. One of the biggest complaints of the companion A.Is is the fact that enemies can't see them during the stealth sections of the game. If Naughty Dog doesn't have the technology to code smart enough A.I, then I think they should stick with a lone wolf protagonist in order to enhance the immersion of their game. Having a lone wolf would also enhance the horror aspect of the game because there would be a fear of isolation as oppose to having the comfort of traveling with a companion A.I.
And to make the immersion and horror of the game feel more personal, I would kinda like the protagonist to not talk so much. Seeing a video game world from another character's eyes makes me as a player feel more of a spectator as oppose to a participant. Instead of using words, Naughty Dog should choose a more sublte narrative design to tell a story. The sewer section was a great example of subtle story telling since there were a lot of empty rooms that showed the aftermath of what had happened. I'm not saying that the protagonist shouldn't talk at all. Silent Hill 2 for example does a great job of telling a story from another character's eyes while still keeping the immersion as well. Of course, narrative design is really subjective to everyone, and I know that Naughty Dog likes to tell stories by using dialogue a lot. For me personally, I just don't like how video games are telling stories by using a more cinematic appoach. We already have movies for that. Video games on the other hand is a medium that can allow people to immerse themselves into a story from their point of view. I really feel that The Last Of Us series has the potential create an immersive world like no other.