A few days ago The Last of Us Creative Director Neil Druckmann revealed during an AMA on Reddit that Sony is giving the studio full freedom in deciding whether to shoot for a sequel of the game or to move on to a completely new IP, but apparently, as Druckmann himself told Wired in an interview, there's more to the pretty peculiar relationship between the Japanese publisher and the prominent first party studio. Naughty Dog has complete freedom in basically every aspect of game design, and that also means that they're able to include in their games elements that publishers would normally shy away from:

We’re very lucky at Naughty Dog that we get to make our own calls. No one outside of Naughty Dog tells us what to do. But I know when it comes to marketing or other aspects of the industry, those calls are sometimes very precedent-driven. So without being able to point to a game and say that can succeed on the market, you’re going to feel a lot of pressure to not do that. We’re lucky at Naughty Dog that we can ignore those recommendations, but in a lot of other studios, I’ve spoken with people in those studios and they cannot. So hopefully—and this is my personal thing, not a Naughty Dog agenda—in doing something like [Left Behind] in the triple-A space, we can help pave the way for other stuff.

That's definitely something you don't see very often in an industry where publishers normally lord over developers with an iron fist, often forcing them to rush titles or to include or exclude this or that element into their games for marketing reasons.

This may very well be one of the secrets behind Naughty Dog's success. When you're not shackled by marketing and pseudo-political decisions outside of your own, there's definitely a lot more you can do to make your games unique.