Middleware engines have become the norm and if Nintendo wants to improve third party support next time around they need to make sure those engines are on their hardware.
They can't--not any more than they could force any other game developer to develop for the Wii U. This is a decision that each developer makes for itself.
In this case it even seems like the dev would be happy to release the game on the Wii U, they just CAN'T. It just isn't feasible for them to jump through Nintendo's hoops.
These aren't hoops that Nintendo have set up. This is like learning German and then being upset that no one can understand you when you fly to Spain. German's a fantastic language and has many intriguing features and so on, but if you can't speak German in Spain, it's not because Spain set up hoops for you to jump through.
To a certain extent, having a different architecture is going to create more work for developers who may only want to optimize for one or the other. That's not a malicious design decision either, but it does mean that a developer somewhere is going to have to make adjustments and compensations. Where middleware is involved, the middleware developer is responsible.
The success of Steam on Linux (two years in advance of the SteamOS-based consoles coming this Fall) has encouraged more and more developers to consider cross-platform tools when they develop new games. With luck, this will have a spill-over effect on consoles as well.