Seems like downloadable retail games on the eShop will be the same price as the retail copy. However, retailers can sell download codes at a discounted price if they choose to do so. So different retailers may offer discounted prices for the download code.
Read my original story on Fictionpress (Shinigami Twin): http://www.fictionpress.com/s/2996503/1/Shinigami-Twin
As well as my other one (Hell's Punishment): http://www.fictionpress.com/s/3085054/1/Hell-s-Punishment
Nintendo Network ID: kingofe3