I once did an assignment on what it's like creating a store.
You had to design floorplans, purchase utility, get permission from the government for where you're opening etc. It's not easy.
retailers are reducing the size of the 3DS and Wii U sections in their stores (even going as far to return shipments of Wii Us to show negative sale numbers), so my question is:
Now why would Nintendo open their own stores when their current products, according to actual retailers who have already taken on these costs, don't think it's worth it to hold onto great stock? What would Nintendo do different?
Even before you factor in the price of creating retail, when you open a store, you expect to sell stuff. Nintendo would have to market these products to begin with, but they can already do this without sinking money into retail.
A Nintendo store might have made sense when the value for buying into their brand was high and if Nintendo was looking to sell other stuff (a store doesn't just contain 3DS/Wii U. If it's like Wal-Mart, someone going into the store could walk out with a 3DS and a Microwave).