(not a teacher)S2 doesn't sound right. To keep it in the same word order it would have to be:"What is it that you really want?"I'm not sure if S2 is grammatically incorrect. It could sound plausible if you read it the right way, but trying to use 'what' twice in the same sentence just sounds weird.Suffice it to say that you'll never hear a native speaker say S2.
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