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Black and White moved a lot more copies than Black 2 and White 2, so Hilbert received a great deal of more attention. Also, Hilbert has a more traditional outfit and hairstyle; like it's conceivable you could see a young male dress like this and have a similar hairstyle. And, of course, there's N, so that ups Hilbert's exposure a lot because of the shippers that draw/write him with N. Personally, I like both but feel free to disregard that opinion because I'm a fag, lol.
The girls though will almost always overshadow the boys because of the demographics that make up the fandom, so that doesn't do Nate's popularity (or lack of) any favors, either.