One other thing I thought about. I've been playing the metroid game with the stylus for a couple days.
When you're using the stylus and have smallish hands, the balance is pretty awkward. You don't notice this demoing it in the stores where the DS is on a stand, but if you put it on the table for balance, then it's hard to reach the shoulder buttons.
It's not a killer deficeit, especially if you have big hands, I guess.
The other thing is I wonder how often we'll run into bad game design.
Things like stylus controls hidden when you use the stylus in your left hand. And games where you end up having to quickly throw the stylus on the floor to hit the a button and then dive after the dropped stylus.