I think that would be pretty cool, but two major problems:
1) The technology. Smart Phones might be able to emulate GB/GBA games, but DS or 3DS even?? I dont think they would have the specs to accomplish that, and since the DS/3DS games use two screens it would not look that well on a phone.
Nintendo started realizing that the 3D capabilities of the 3DS weren't as good as they hoped. Most people I talk to who have a 3DS tell me that they turn the 3D function off. I do as well; 1. because it hurts the eyes and 2. because it slows down the framerate. It's one of the reasons why Nintendo released the 2DS (the other reason being because of poor console sales, the 2DS was an attempt to re-invigorate the market and that's only been slightly successful. Currently Nintendo is running at a net loss in profits. If they don't do something they could go the way of Sega.
To address the 2 screen function is actually pretty simple. You simply make the 2 screen format a slider. The default screen would be the main playing screen, but when you need to use the functions on the lower screen you simply "slide" the screen up. But also let's not forget that the primary purpose of the lower screen is to be used as a touch screen. This functionality is already present in all smart phones and tablets. So having two screens for this purpose isn't necessary.
2) Nintendo/GF. I really dont think they would publish any of theri IP on anything else than a Nintendo console. They never have, so why would that change now?
The same was said of Sega. At the height of Sega's popularity it was stated by fans of the consoles that Sega would never allow their games to run on anything other than Sega consoles. But Sega soon realized that the drop in their console sales was dragging them down. They had to decide whether they wanted to invest more in the hardware and focus less on software, or put all their attention on the software. We know which decision they chose, which is why we now see Sega brand titles on other platforms. A wise decision in my opinion.
Despite all the good things about the Nintendo 3DS console there is, it alone cannot sustain Nintendo. Nintendo's WiiU flop has hurt the company tremendously and the company's 3DS sales is insufficient to let them operate at a profit.
Time and time again it has been shown that dependence on any one platform has jeopardized a company's future. Compaq, Dell, and HP realized this when their computers once only supported components from those companies and you could only buy upgrades from them. They realized they were losing out to the generic computer companies because those companies did not rely on any one brand. Customers could pick and choose what they wanted in their computers. Now that those computer companies have allowed greater flexibility in their computer systems, their brands are once more popular with customers.
The same, I feel will be true of not only Nintendo but Microsoft and Sony as well. There is only so much gamers can expect out of the machines they own. They're not upgradable and therefore their lifespans are quite limited. Not to mention very expensive.
No, the answer, I believe, lies in portable devices that are relatively inexpensive, offer the ability to be upgraded, and can run a wide assortment of software. Already the processors of these portable systems are getting faster and I don't expect it'll take long before they surpass the processing power of even the most powerful gaming console.
If Nintendo cannot adapt. It will go the way of so many other companies. I am not a stickler for any particular system. What matters to me is the games I play. I don't care if the game is on a PC or an Android phone or on a gaming console. I don't pick the games for the console. I pick the console to play the games.