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I think it's because somehow, there's a very human element about Ryoko.
As much fanservice and as much as she plays up as comic relief, she's the most believable and likable member of the cast.
Despite the rather batshit looks, there is a Ryoko in every workplace: A woman who's done horrible things who knows what she wants and that thing is someone but she knows she'll never have it.
It's a crux of most interesting classic stories, actually, in conjunction with a good mind-fuck or something educational (leave string in mazes, don't fuck your mom, don't anger the gods, if you don't know what it does don't fuck with it, don't leave things in the fridge, etc).