There's actually a very reasonable explanation for this stuff going on, though it's not just Gamestop. It's really any big retailer. This is how things was back when I was working at Game years ago, and it still is the case today when I'm at Gamestop.
Shelf-space is paid for. It really is that simple. Microsoft and Sony are willing to pay more for extra space, and retailers are willing to give them that. That's not to say that all retailers will have less space reserved for Nintendo-titles, because in some cases, stuff like this is handled locally. Gamestop might look at their sales in one part of a country and see that Nintendo games sells better there compared to other areas, and they'll relay that information back to Nintendo with the hope that they'll think it's worth it to pay for more space.
At our store we have a very obvious focus on the Playstation 3, and it's because most of our customers are PS3-players. We sell shockingly little Nintendo-titles, and most of the people who buy them come back the next day complaining that their new Wii U game didn't work on their Wii. But because of this, we've got half of our store filled with Playstation-stuff. Microsoft gets a little more shelf space than Nintendo, but we sell very little Xbox-titles as well.