As mentioned already, a revamped (or really, institution thereof) online infrastructure would net wonders for Nintendo. Develop a unique ID that can log in on Wiis, Wii Us, 3Ds, and the web. Yes, MS and Sony beat you to it, Nintendo. Swallow your pride. From there, link all my old and new game purchases. Develop a great friends list and pimp the 'now playing' / 'recently playing' functionality to spread intrest in the VC through that social network.
I'm wary of digital sales. Part of me just doesn't want to see someone getting NES Pinball for free with I paid $5. But, more realistically, I wonder why on the earth I paid $5 in the first place. But I do agree with Iwata's GDC comments about digital shifting value perception too far downwards. On the flip side, they're gifting games based on Nintendo points (ala PSN ), so there is a middle ground.
Making any changes to the rom - especially on the scale of 3DS classics (e.g. Kid Icarus example above) - is unrealistic and unwanted by me.
Lastly, while I understand wanting that stream of new games to scratch your itch, have we all beat FF 3, Chrono Trigger, Breath of Fire 2, Super Mario World, Majora's Mask, Faxanadu, DoReMi Fantasy, either Ogre Battle, Super Metroid, Rondo of Blood, Megaman X, Sin and Punishment, MUSHA, Phantasy Star IV and Shinobi arcade already? Because....