Final Fantasy games are plenty dark and mature.
They aren't splatter-shooters and gore ridden but the story themes are pretty darn serious most of the time.
Just think of Final Fantasy X. Yuna going on a pilgrimage with the goal to sacrifice herself, getting to know life, friends and in the end losing the one she loves.
I cried pretty hard when she stumbled through Tidus' shade and fell down. (I pretend that X-2 never happened *cough*)

Also look at Yeuls fate in 13-2, see how the "bad guy" loses his sanity from seeing her die over and over again. Not to mention that ending hitting like a 40 ton truck out of nowhere.
See Rinoas self doubt take shape in VIII.

Final Fantasy VII features the most memorable death of a beloved character I've ever seen. Also in the remake, dear God I never felt so strongly about a bad guy before. When Hojo talked to Aerith about what he did to Ifalna, I wanted to reach into my screen and tear him apart. Not to mention the whole issue of reckless use of technology destroying the planet.

Bottom line: games don't have to be like Doom 3 in order to be dark.