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You're right, story doesn't change gameplay. Actually, story is the reason we play games, and why we read books, and why we watch movies, and listen to music (especially ballads, folk music and epic poems). Awesome story is a prerequisite to having a good videogame, but unfortunately most developers skip that step. The story is what makes us care for the characters and. Tetris is fun, for example, but you can't put any emotional stake in it, like you can in Halo.
Art design and, even more importantly, sound design are aesthetic choices that make huge differences the way people feel about games. Disregarding aesthetics is like saying there's no difference between Eragon and Star Wars simply because you can find similar plot lines. You can debate the rationality behind it, but I guarantee the vast majority of gamers would enjoy Halo less if it had little cubes instead of intricately modeled weapons and armor.
Sorry, as an amateur game designer I had to rant a bit
