I know of Wario Ware DIY but is this the only option?
Nintendo supports developers with their DSiWare and WiiWare for people wanting to make a game downloadable through the console or handheld.
The first step is to contact Nintendo to become a licensed developer (http://warioworld.com/). After you've made this important first step then Nintendo will be able to answer all of your questions.
Be prepared that they will want you to demonstrate your ability to make a fully playable game for the platform, as well as information about your company for approval.
You can write your own games from scratch for many of the Nintendo platforms. devkitPro provides devkitARM, which can compile for the Gameboy Advance and the Nintendo DS, as well as devkitPPC, which can compile for the GameCube and the Wii. There are also utility libraries to help you access the hardware.
Running your games is very simple on the GBA and NDS, you simply buy an adapter that will load the compiled games off of a microSD card. It takes a little more work for GameCube and Wii, but it's not too bad.
(Unfortunately as of this post, the devkitpro.org site seems to be in the middle of rebuilding? All the usual download links and info pages seem to be missing, it's just a plain forum.)
Unity provides Wii and Wiiware licenses but, I'd imagine they come at a hefty price. Still if you have the cash, it is a great environment to work in.