Nintendo could just allow indie game developers to publish their games via 3DSWare for free. That's what already happening on iPhone and Android. Then, we would have something resembling "homebrew" without the need for cracking the console.
Of course, Nintendo will never do that, as they are more paranoid about SDKs and game studios than Apple...
Concerning the flashcart discussion:
To allow homebrew, you need to A.) be able to execute custom code.
To allow game piracy, you need to B.) dump ROMs and C.) feed them to the console.
You can imagine a situation when you have one but not another.
On PS3 running their Linux, you have just A - homebrew but not piracy.
On Xbox360 with flashed DVD, you have just B and C - piracy but no homebrew.
Of course, Nintendo will never do that, as they are more paranoid about SDKs and game studios than Apple...
Concerning the flashcart discussion:
To allow homebrew, you need to A.) be able to execute custom code.
To allow game piracy, you need to B.) dump ROMs and C.) feed them to the console.
You can imagine a situation when you have one but not another.
On PS3 running their Linux, you have just A - homebrew but not piracy.
On Xbox360 with flashed DVD, you have just B and C - piracy but no homebrew.