Ok, let's play along.
How would you justify one less income stream? What would make me buy two copies of MK? Two copies of DK? Two copies of NSMB?
How many people are actually buying 2 copies of the game for handheld + console right now?
And how many of those are there actually available?
Two copies of New Super Mario Bros? NSMB/Wii + NSMB/DS are not the same game at all. Super Mario 3D Land + World are also not the same game. Those are 2 completely different games.
Xenoblade Chronicles on 3DS + Wii, that would be a point. But it's also a niche game. And Nintendo could have saved money in case they could have simply released it back then on handheld + console at the same time without any real effort on their side.
By combining those platforms, they can sell one of their games for handheld + console, which means for every game there is a larger audience available than right now.
Just think about this: Super Mario 3D Land on Wii U. And Super Mario 3D World on 3DS. If you own both, you could play both of those on 3DS + Wii U. I think this would be a great feature for people, that own both. And it would also be nice for people, who own only 1 of either Wii U or 3DS.
Let's say you absolutely love Super Mario 3D Land, but you also only own a 3DS. Now you see that Nintendo released another game like this and you want it. Currently you have to buy a Wii U to be able to play it. Which means the customer has to spend way more money. And there's a chance, that the customer will not buy it because of that.