Later this year, Pokedex 3D Pro will be replacing the current free version on the eShop. Starting August 31, an update for Pokedex 3D will be going live. This update will unlock 6 Pokemon including Reshiram and Zekrom. All other Pokemon will be available for download through SpotPass which includes alternate forms.
When the update is live you will be able to press an update button inside the application to download the content.