Spoilers
Neil and Bruce also talked about how they knew two things early on in development, with the first being that Joel and Ellie would have inverse arcs. This involved Joel getting his humanity back, with Ellie becoming corrupted, while also coming of age at the same time. Along with this, they had planned for Joel to become incapacitated at some point, with Ellie becoming the guardian.
Secondly, it was always planned to have The Last of Us be episodic, interacting with different characters along the way.
End Spoilers