Visionary development teams sometimes walk into the sunset once the story arcs of their games' cast have concluded, or if they feel there's little left for the IP to say. Despite this, and especially in the case of massively popular series such as Uncharted, there's probably way too much money on the table for it not to continue in some form. Recently Naughty Dog discussed exactly that about the Uncharted franchise in a post-Thief's End world.
Speaking with Game Informer about the upcoming Thief's End expansion The Lost Legacy, Naughty Dog co-president Evan Wells had the following to say regarding the franchise's future and fate once the expansion is released.
I would say that Naughty Dog doing an Uncharted after this is unlikely. I would never say never, but we've got The Last of Us Part II on our plates and there's so much other stuff that [we want to explore]. It'd be hard. If we magically had that two-team, three-team studio, sure – it'd be great to keep doing it. We really love the franchise, but the studio has limited resources and lots of other ideas. I'd say the likelihood is low.
Of course, this still leaves the door open for other studios to take the reigns; after all, Sony Bend did a respectable job with Vita's Golden Abyss, and were a similar effort afforded more time and non-handheld status, the results could be quite impressive. Such a choice would likely be controversial, so we'll see where Naughty Dog and Sony decide to take things. Who knows, perhaps Wells and his team will have a change of heart.
Uncharted: The Lost Legacy was announced by Naughty Dog in December of last year, and is scheduled to release sometime in 2017.