Capcom announced today that Mega Man Legends 3: Prototype Version will be one of the first titles 3DS owners can download from the Nintendo eShop. Capcom is asking people who play Prototype Version to leave them feedback and ideas, with the prospect of fans getting their ideas and name put in the final release of Mega Man Legends 3. No official release date has been announced yet.
EDIT: As of July 18, Mega Man Legends 3, along with the Prototype Version, has been cancelled. Capcom stated that the project 'did not meet necessary criteria' and the decision was made that the game would not go into production.