As said, FF has been delving into darker subject matter pretty much since the beginning. War, death, politics, religion, etc. have all been mainstays in the series. It's now just that they are appearing to depict the violence in a clear visual way and aren't really flinching or shying away from it as much as they used to. Of course, most entries in the series haven't existed in a time where the graphical capabilities of the titles were up to showing properly detailed and animated character models so even if there was something going on they couldn't really show it.

So, yeah, the darkness has almost always been there but it hasn't always been really clearly demonstrated on screen.