I think they understood. It's just that there were forces beyond their control, or at least sacrifices they had to make.
For example, I suspect that the 3DS absorbed a lot of development resources that could have gone to the Wii U. Whereas the DS had reached running pace by the release of the Wii, the 3DS was still having problems late into 2012. Hence, more development resources for 3DS games.
Kid Icarus: Uprising, much as I love it, is the reason why Super Smash Bros 4 was not a Wii U launch title. Paper Mario: Sticker Star could have been an early Wii U title, but the 3DS was short on RPG's in its early life, so it became the first handheld entry in the series. And of course, NSMB2 required extra work from the same studio that made Pikmin 3, likely causing the game to be delayed by months. Fire Emblem: Awakening could easily have been a console game, like Radiant Dawn before it.
Imagine a scenario where Nintendo said "Screw the 3DS, we'll let it survive off of Animal Crossing, 3rd parties, and 2011 titles this year." Their launch lineup would have likely included a 2D Mario, NintendoLand, and Super Smash Bros 4, which could also have come out on the 3DS! Fire Emblem: Awakening would come out early in the system's life, probably in Q1 2013 in Japan at least, giving the system a notable RPG quickly. LEGO City Undercover would come in at the end of the financial year, in march. As Spring and Summer came, Pikmin 3, Game & Wario, The Wonderful 101, and Paper Mario: Sticker Star would come out every so often. And finally, during Q4, we'd still have Super Mario 3D World, Wind Waker HD, Wii Party U, and Wii Fit U.
That's over a dozen games by the end of 2013!
Why was 2013 different than 2007? Because by 2007, the DS already had all of its big sellers: Nintendogs, Animal Crossing, and Mario Kart came out in 2005 and Brain Age, New Super Mario Bros, and Pokemon G4 came out in 2006, at least in some parts of the world. In the beginning of 2013, the 3DS was in a worse situation: 3D Mario had become a bigger deal for the 3DS than the DS, but Brain Age and Nintendogs had declined drastically, and Pokemon simply wasn't out yet. So Nintendo had to split their resources, something they're not very good at.
In short, if the Wii U had to be released in 2012, either it or the 3DS had to pay the price of coexistence.
My personal opinion: Nintendo should have released the Wii U fairly much like it is, but at least a few months later, maybe even in Q4 2013. Nintendo would simply make a couple more games for the Wii (Pikmin 3 could have been their big game for Holiday 2012, NintendoLand and Game & Wario resources could be used in other ways, etc.) Meanwhile, when Holiday 2013 came around, the Wii U would launch at $300 bundled with one of several killer apps, like a 3D Mario, Wind Waker HD, Wii Party U, and Wii Fit U. The Wii U would lack the post-launch blues of real life, with Donkey Kong and Mario Kart coming along soon afterwards.