I'd argue that Dark Souls and Bastion, for example, have too little story to really be considered more than atmosphere

Then I suggest you pay closer attention then, because their worlds are actually quite well-fleshed out. Dark Souls has an entire mythology and timeline of its world if one cares enough to look for it, as does Bastion, pieced together from the people back at the bastion and from that disturbingly sexy narration.

To me, a good cinematic story is simply more fulfilling. It sounds like you don't particularly care for cinematic storytelling in games, which is fine, but many people do, and that's what someone like Naughty Dog is going for.

That's fine; different strokes. But I don't see why we use "cinematic" as a positive term in video games; we should not be attempting to ape cinema, we should be trying to do our own thing and prove that our medium doesn't need to rely on the tricks of others to survive. David Cage can scream about how "cinematic" Indigo Prophecy or Beyond: Two Souls are because he's cut out all but the essentials of that pesky gameplay, but it hardly stops me from calling them pretentious rivers of quicktime events and spunk. Ubisoft may claim that Assassin's Creed is more "cinematic" at 30 FPS, and I can also claim that they're full of crap and are trying to make excuses for a buggy, rushed and unoptimized game. Forget "cinematic", I want "videogame-atic".

The other poster used Lord of the Rings as another great example of this.

The movies, perhaps. As I also pointed out, if the books were released today, they would be critically mauled for having absolutely no character. Tolkien is romanticised by the geek community, and not without merit, but his characters are about as shapely and fleshed out as a piece of two-by-four. The live-action films circumvented this problem by putting a much stronger focus on characterization and emotions and toning down the absurd nature of the set pieces.