There were a lot more "exhibit" type displays before Nintendo opened an actual museum. A lot of that stuff moved over there, like the Game Boy that survived a war or whatever.
It's an okay store or whatever. There are a lot of items that you can only buy there. I've definitely gotten a few hats that were pretty dope.
I haven't gone to one in a while, but the Nintendo store used to be fun for certain game launches. I think the last one I went to was for Scribblenauts, and that was super fun.