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I know easily twice as many Nathaniels as I do Nathans, so if the ease that you're considering comes from it being a shorter name, I wouldn't worry about it. Nathaniel's a pretty easy one for people to grasp. If your preference for Nathan isn't that strong, and you both agree on Nathaniel, I recommend going with Nathan as a nickname.

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As a matter of interest, without exception every Nathaniel or Nathan I know goes by Nate. And after Christopher and variants of Eric, it easily competes to be one of the top most popular names of my personal acquaintances.