I mean, it’s an FPS as well as an RPG. Unless you’re going for a melee build, a Mouse is still going to be more comfortable for Guns or Energy Weapons builds.
…how? It’s a game, that you play, with a first person perspective, and shoot guns. Unless you only use VATS, a mouse is going to be more comfortable for most people, myself definitely included.
I don’t use V.A.T.S. at all; never have. Getting a decent gun early game and going for headshots has served me well.
Not everyone considers “sitting upright or hunched over at a desk as if working” the most comfortable position to game in and it’s not like you need the extra precision of the mouse to enjoy a story-driven RPG like you do when playing a competitive FPS that’s only about precision and reaction time.
