I have only quickly browsed over this thread, so I don't know everything said. But I get the impression that many of you don't understand how I think such a feature would work.
Firstly, to implement such a thing is NOT a difficult thing, AND no actual games even need to be modified. You see, the only core thing that needs to be done, is to Send/Receive Player Control Input over a Network/Internet. The other important thing is to ensure each players Virtual Console is in synth with each other, which again I don't think is a hard thing.
Now obviously you would have the ability to play any physical multiplayer games online, as if your playing against someone sitting next to you. Take Goldeneye 007 for example, the screen would still be split, and you would be able to see each others screen .
So even though I think it would be such an easy feature to implement, it will still be interesting to see if Nintendo support the idea. I myself have no idea of any Busniess and/or Quality issues may stand in Nintendo's way as to avoid this feature. Maybe others can think of some? I guess we will just have to wait and see :-\.