Well, let me tell you. It's a magical place with Pokemon goods as far as the eye can... actually I'm just joking with you. :P I can't remember how the Pokemon Center looked very much anymore. The Nintendo Store has the same layout, though, so I'll use that as a template.
There's two floors, but the store itself is relatively small (about the size of a fast food restaurant, maybe a double decker McDonalds or something). The ground floor of the Nintendo store is still dedicated to Pokemon. As you go upstairs, you'll set cutouts or something of various Nintendo characters, probably all Mario, I can't remember. Then it's got Kirby plushies to the exact right of the stairwell. Normally, this'd be a great thing for me, except they were all based on that terrible anime. Next. Immediately right past the Kirb-dolls is a display case of either game cartridges of all the Nintendo systems, or the systems themselves. In the area in front of that, shirts and bookbags, same junk you can get at Target/Walmart/Hot Topic/Toys R Us. Left of the staircase was some gaming booths, I saw SSBM was one of them, I suppose they may hold tourneys. Straight ahead was a place to buy actual games, nothing special. I think there may still have been a place for Pokemon comics, but mostly the Viz publications.
The ground floor, Pokemon plushies near the stairs, figurines against the back wall, more plushies surrounding this circle like table in the center where I think you could playtest the newest Pokemon game, whatever that was like two years ago. Also, they play Nintendo game music while you're in the store. I picked up on something from The LoZ. Seeing as this trip took place the summer of 2011, I didn't get a lot out of it aside from a Mew and Lapras plushie because everyone else was unfamiliar Pokemon wise to me (and again, didn't like what the Kirby stuff was based off of). Oh yeah, and somewhere in there was a Nintendopoly board game, which I only recalled because it also used the terrible anime designs for Kirby references.
My sister warned me that the store was nothing special. She was in NYC for an internship, and had already checked it out. We were both there before when we were younger and it was the Pokemon Center, so I believed her. Still, I wanted to see the changes for myself. I met up with her and my dad later, and she really couldn't wait to get the look of indifference on my face on camera when we walked in. It's so very mediocre it's not even funny. The Toys R Us in Times Square is way better, and has a video game section nearly identical to the Nintendo Store, but better in the sense that it's not just Nintendo.
Well, here's a picture of the exterior, anyway. Ignore Nidoran. :P