Vision of Escaflowne would, in my mind, qualify as "good" fantasy anime. (Not the manga.) But again, the interpersonal relationships and characterizations are what distinguish that story.
If the plots of .hack or Ghost in the Shell appeal to you, you might try Spirits in the Wires, by Charles de Lint. I think most people would consider de Lint a "fantasy" writer, but his people and conflicts tend to be very believable. You can consider them, if you like, stories from a slightly-alternate Earth with slightly different-- but plausible and oddly familiar-- rules from our own.
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