Since 3DS's launch, a number of design design flaws have become apparent to Its owners, including myself. In addition, developers like Capcom have been unhappy with the default control options available for the machine, prompting Nintendo to develop a cumbersome add-on Circle Pad. These two things strongly suggests the handheld was rushed out to consumers and that developer input was not heeded during it's development. The latter is exactly what Nintendo is claiming is happening with WiiU however. I can only guess 3DS missed out on the fresh approach of courting developer input.
"We are also planning to launch the Wii U, which is the successor to the Wii, during the next fiscal year. We would like to show the final format of the Wii U at the E3 show next year. As we learned a bitter lesson with the launch of the Nintendo 3DS, we are trying to take every possible measure so that the Wii U will have a successful launch."
Reggie Fils-Aime talks about this in an inteview with GT (15.00)