@Neox Substance Designer can be used to make shaders, MDL for example and there's ongoing work to integrate MaterialX. To the OP, we have lots of resources to help with understanding how Naughty Dog does their textures: https://polycount.com/discussion/122359/the-last-of-us-art-dump-rogelio-olguin/p1 Great post from…
See also the Vertex series of books. It features some artwork and breakdowns from Naughty Dog, like Anthony Vaccaro who did environment art for the Uncharted series. https://ryanhawkins.gumroad.com/ And we have more Naughty Dog game art examples here http://wiki.polycount.com/wiki/Game_Art_Examples#Uncharted_3_.282011.29