In theory, 3DS titles are meant to be priced the same for their package and download versions. In theory.
In practice, retailers appear to be pricing the download versions higher than the package versions.
Joshin Web, one of the few online retailers selling download codes for full 3DS games, lists the MSRP for both the package and download version of New Super Mario Bros. 2 at ¥4,800. Like most retailers, however, Joshin offers a discount over the MSRP. The package version is discounted to ¥4,130. The download version's discount is much lower, bringing the game to ¥4,580. These are both tax-inclusive prices.
Joshin Web also gives package version buyers more points back, at 124 points for the package version compared to 46 for the download version.
Furu 1 Online has a simliar pricing discrepancy: ¥4,179 for the package version and ¥4,559 for the download version. Package buyers get ¥250 worth of points back while download buyers get just ¥46.
The pricing and point discrepancies at both shops are similar for Demon Training, the other game that kicks off full 3DS title downloads on July 28.
Package buyers who chose to buy online will have to pay shipping, which is usually below ¥300. Many shops offer free shipping specials. Furu 1 Online is offering free shipping on purchases through July 26, for instance. Of course, if you're buying the package version, you can also go to a general electronics store, which will will also usually give a discount and points back.
Buyers can also opt to buy directly from the 3DS e-Shop. Opt for this approach, and you'll pay the full MSRP, without any points back.