Oh, I agree completely. Your last paragraph is exactly why this letter from the people who made Threes sound so particularly whiney. They have forgotten that they don't get to tell people how to enjoy themselves. Any parent who has watched their kids play with the cardboard box more than the toys that came in it will tell you that.
I don't think we can know why 2048 became so popular and Threes fell in its own shadow. Maybe it's a sign that open source and free as in freedom have finally registered with the general consumer on an emotional level, though I doubt it. If we knew for sure then we could make such better toys that the kids ignore the box.