I think this pricing structure would be fair. Every game is basically released in two versions (available through retail 3DS sized cartridge or eShop download):
$49.99-$59.99 for "high end" version - You buy this one and it plays on the console and handheld, simple, straight forward.
$29.99-$39.99 for the "portable only" version - You buy this version and its only for the handheld. But you can "upgrade" it via the eShop any time for an additional $10-$20 anytime (similar to how Nintendo handles VC download transfers on Wii to Wii U ... you pay an extra fee) if you choose to buy the home version NX and want to play on your TV down the line.
Fusion being a different type of platform concept would require a little more thought given to software pricing, but that's not a bad thing, it just means its different.
