I think Nintendo's most painful problem is their inability to do digital distribution well enough. Arguably, they have/can crush it sales wise when it comes to making games that come on discs/carts and go in their hardware. I think the mobile phone world, specifically iOS has a lot of potential usage for plying their back catalog of NES, SNES, and GB/GBC ports (last time I looked Android had more emulators than you could count, so no need to bother there). I think the idea that Nintendo would make original content for phones is a farce, but building more goodwill among the folk who aren't buying Wii U's or don't realize yet that they want a 3DS with more full featured mobile gaming, couldn't hurt. As it is, the Virtual Console situation is downright abysmal. Let someone else, namely Apple, handle a bit of the digital distribution and rake in the money with ports of Super Mario at $5-$7 a pop.
As for the touchscreen control issue (that Jeff has mentioned in podcasts previous), I think there's enough finesse for most games when done well. Super Crate Box and League of Evil are extremely tight platformers on iOS that use touchscreen d-pad and buttons very well. If they were willing to put a bit more work into the ports, they could add bluetooth/wifi networking for multiplayer. Hell, that exists now in emulators, and is perfectly serviceable for a game of SNES Mario Kart over the internet. Obviously Pokemon Red/Blue also comes to mind, and could leverage networking as an excuse for a higher price. I mean honestly, if Square Enix can get away charging $10+ for mediocre ports, Nintendo could surely do better than that.