All this will lead to is higher price accessories, and more unlicensed homebrew ones.
The Nintendo/Atari story is of no relevance, because it applies to SOFTWARE not HARDWARE. Requiring SOFTWARE titles to be licensed is one thing. It gives control over game content to the console manufacturer. Wether this is good or bad depends on how tight a grip they maintain over the process. It worked for the NES. And there are still a lot of homebrew UNLICENSED games around.
Hardware licensing will prevent people from using the XBOX any way that MS doesn't want them to.
That being said, the XBOX 360 will probably kick ass, just like the XBOX. But I probably won't buy one for the same reason I don't own an XBOX: Microsoft.