Not a good justification, but I think the reasoning probably goes like this:
(1) controllers can double as Wii classic controllers, which don't need long cords; personally, I like the fact they aren't super long because it makes the controllers more useful in different contexts
(2) longer replacement HDMI cables are something Nintendo can leave for customers to purchase; what's in the box is workable and anyone who wants more can easily find a replacement
Fair enough, but two feet is just silly, that's too short to even have the system sitting on the coffee table and sit back comfortably on the couch, at least the way my living room is set up.
And even when you were a little kid you were forced to sit close to the TV.
When you're a little kid, you don't care about things like that. Sitting on the floor two feet in front of the TV is something you do by choice, even when your parents tell you not to. As an adult in your 30s, which is the demographic they're going after, that's not so appealing anymore.
I realize it's not that big of a deal but it's still a bad decision in my opinion and all of the reviews and podcasts discussing it seem to agree.