They're not going to make the exact same game that you buy once run on both. This may happen, but it'll be the exception, not the norm. Handheld and console user experiences are two completely different things.
Console = Big game, sit down for a while
Handheld = Smaller game, played in bite size chunks
You can see this again and again in all of their handheld and console releases.
At this point, the biggest differences between the two are scale and production values. You're also much more likely to see really significant multiplayer on consoles.
Compare the handheld NSMB games to the console ones. Compare SM3DL to SM3DW. They're all games that you can play in basically the same way, with the main difference that the console ones have better production values and multiplayer.
Compare Ocarina of Time 3D and Majora's Mask 3D to Wind Waker HD and Twilight Princess HD. Or, as an older example, compare Link's Awakening to A Link to the Past.
Compare handheld and console Mario Kart entries.
etc. etc.
Even in the big "console-sized games," you'll often see Nintendo go out of their way to introduce modern conveniences that would make most of those games more than playable on handheld hardware.