Yes but not in the way people think IMO.
Lets take a standard game like Super Mario Galaxy 3. All games ship on 3DS/Vita sized cartridges, which can range in size, 4GB-32GB by next gen (most Wii U games are under 16GB).
Mario Galaxy 3 - Console Edition $59.99
Mario Galaxy 3 - Portable Edition $39.99
They're the same game, except the portable version runs at 960x540 resolution lets say, and the home version runs at full 1080p with a few extra graphical flourishes. If you buy the more expensive console edition, it's $59.99 it works on both the home and portable Fusion right out of the box.
If you buy the portable only version it only works on the handheld version *but* you can always go into the eShop, pay an extra $20, and "upgrade" to the console version at any time and voila, now you have the console version and can play on the home Fusion too (for TV play). Lets say you buy the home Fusion model 8-9 months later and you want to be able to play your copy of Galaxy 3 on your TV in 1080p ... well just go into the eShop and pay the extra $10-$20.
Kinda similar to Nintendo's policy for Wii VC - to Wii U VC transfers, if you owned say Super Mario World for the Wii (VC), to get the version on Wii U didn't require you to rebuy the game, but you did have to pay an extra fee, that was like 1/3 the price to get the Wii U version which had gamepad play.