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.
If you want to do it free, there are three options I know of as of now.
- The devkitPro toolchain has support for the Wii, GameCube, Switch, 3DS, DS, Gba, GP32, and PSP.
You could also you devkitadv which lets you develop for the GameBoy Advance, but no others. DevkitPro never worked for me, sadly. You could also get in through the Nintendo developer portal and Unity. However, that requires you to be 18 years or older. So if you are an enthusiastic teenager who wants to develop games for their 3ds or Wii U, you will not be able to do so through the Nintendo Developer Portal. Speaking of which, that method only supports the 3ds and Wii U at the moment. And when it comes to the 3ds, it also only supports the "New" variant.
There is finally, the option to program in a systems native assembly language. This is probably time consuming and less user friendly, but it is probably the most guaranteed to work. I am also not sure how accessible programming in the native assembly language would be. I hoped this gave you or another person some ideas for options when developing for Nintendo systems. I myself have never done it, but I know of a lot of options out there.