What's actually worrying/confusing me here is how NCL/NOA plan to deal with 3DS NES downloads. Before announcing these NES titles, it was logical to presume Nintendo intended to keep the handheld and home systems separate; if the 3DS had VC handheld titles, and the Wii/WiiU had VC home titles, each set can be continually transferred to the next handheld or home platform. As long as you kept the two sets of VC titles separated, there was an easy "out" to avoid issues of annoyed customers having to repurchase a game.
Now that the 3DS is going to have paid NES downloads, I'm not really sure what (if anything) Nintendo plans to do. It seems unreasonable to expect Wii owners to purchase a second, identical set of games for their handheld systems.