I would LOVE for one or two characters to remain solely unlockable by purchasing both games. It would mean that the Wii U could remain a viable system seller, not to mention allow for an aspect of freshness for the Wii U version, which would have wained somewhat amongst casual players who have played the 3DS version for months and see no reason to buy the Wii U version. Fantastic idea.
Edit: I agree some might consider it 'cheap', but it would also give the casuals a real reason to return to the game months later when perhaps some would not, considering that new characters would then be available that nobody so far had been able to play. Of course, the characters would have to be unlocked in both versions of the game upon buying the Wii U version.