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I think it will be integrated sorta like this ...

$49.99 gets you Mario Kart 9. You can play on the handheld in 540p.

For $10 more you can "unlock" the home dock version which lets you play at home as well at 1080P.

Games are identical otherwise. It's your choice as the consumer. Kinda like what Nintendo did with the eShop ... you could transfer your VC purchases over but for a small fee you got Wii U VC support. I believe this is how some iPhone/iPad games/apps work ... you pay  a certain price for the iPhone version and then can "upgrade" to the iPad version as well for less than the original app price.