They're first adding them to WiiU so that it brings in more sales for WiiU. Then when everyone is done playing gba games on WiiU, they'll put it on 3DS eshop, and people will want to buy them again for it.
Smart strategy, really. Had they put gba games on 3DS first, no one will feel like buying it for WiiU then, but the vice versa is very plausible.
Currently playing: 999, Shin Megami Tensei: Devil Survivor Overclocked, Fire Emblem: Awakening, and Scribblenauts Unlimited