They love helping scalpers thats for sure

Of course they should make more.
Nintendo is not in any way profiting from those artificial shortages.
As it stands now, only a few scalpers are profiting, and that's not how it should be.

Truly limited editions should be something really special and a rare occurrence, e.g. like the recent 20th Anniversary PS4.

Why not both? :P

But I think a lot of this goes back to them keeping their operating costs low.  Remember that last fiscal quarter report?  Yeah, they had to streamline somewhere to get the costs that low. 

Maybe this is an elaborate Nintendo plan, I just bought galaxy 2 (awesome game), and who knows how many people will buy the Metroid Trilogy (I will).

Won't these be New 3DSXLs? I wonder if they only had so many set aside to be limited edition because they want to make sure the production run of the regular versions is set.

who says that nintendo hasnt some people sitting on ebay and selling stuff?

Nintendo is back at profitability. They can play it safe. They always do.

Its basic economics, demand and supply, you create more demand with less supply, yes it does help scalper's but if Nintendo creates more demand for their products they will end up winning in the end, I believe this is what apple do aswell