In the case of Samurai Warriors: Chronicles 2nd, Inside Games say the eShop version will take up 1,800MB of space. Interestingly, Tecmo Koei are pricing the eShop version of the game slightly cheaper than the retail version. The retail version costs ¥6,090 but the eShop version will cost ¥5,400.
Well, this marks the first actual game that’s available for a cheaper price on the eShop than at retail. So I guess price wise, it's up to 3rd party developers to set them. I don't think first party titles will follow suit though, but we will see when time progresses.
SOURCE
http://www.siliconera.com/2012/10/12/akb48-me-and-samurai-warriors-chronicles-2nd-to-hit-nintendo-eshop-in-japan/