If you ask me, Nintendo needs to pull some pure oldskool 1985 crap and limit the amount of people they give licenses too. This shit is just ridiculous.
While I agree with this, do you have any idea the ruckus that would cause? Everyone would start bitching. Look at the people complaining about how the iPhone's new firmware breaks 3rd party apps, and homebrew etc.
If Nintendo did this, they would be accused of not caring about the customer and everyone would come crawling out of the woodwork with comments about how they bought the system, and as such should be able to use any third party stuff they want.
Nintendo is screwed either way, it would seem.