As it has been pointed out Fusion is the only real path for Nintendo.
The reason you aren't seeing 3DS games on Wii U it's because porting is really hard, as Nintendo already admitted. Otherwise you'd see, probably, several 3DS games on Wii U - thus sharing a library even if on a small level.
Fusion strategy noticable today because it just isn't feasible to port from 3DS to Wii U.
But, when both HH and HC have that share architecture, you can bet that a shared library will be the main focus in Nintendo's strategy.
Financially, it's almost impossible for Nintendo to have Nintendo-like-profits without this strategy: one game released on 2 platforms equals less financial resources for said game, one marketing budget and more people to sell it to.
If software sales really are the bulk of Nintendo's profits then it's very important to reach out to as many gamers as possible, whilst spending the least possible.
From a games perspective, it's not just Pokémon that will make it's way to home consoles, it's all those great japanese games that don't get released in the west.
A wider audience should help Nintendo fight Sony for the best console for japanese games.
