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What I think should be realized is that since Rei is (unfortunately) a fictional character, we don't necesserily have to work within established canon when it comes to shipping.
Within canon, Shinji would be the best fit for Rei and vice versa. They need each other to a degree that no other characters do.
But there's no real reason as to why someone shouldn't want Rei for himself if she is his waifu. That's a natural, innate reaction for a man to have. NGE has already gone through various iterations that present differing versions of the characters and of the events, so there's nothing really preventing a person from fantasizing about being the object of Rei's affections and desires.
