The Wii shortages were explained. Nintendo had no idea what the demand would be like. You can't just "ramp up" production on something as soon as the pre-order results come in. It's a decision that has to be made months ahead of time, and the biggest selling time for a console is usually it's mid years, meaning that demand for Wii was going up just as Nintendo was struggling to keep in line with the demand. With Wii U, they probably thought there wouldn't be much of a demand, at least not on the scale of what the Wii had.
I'm sure Nintendo also doesn't want a repeat of the GameCube where there were so many of them sitting in warehouses and on store shelves that they had to temporarily stop production on them in early 2003.
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