Well, we finally have official confirmation as to why the screen is stylus based and not multitouch based.
http://www.gametrailers.com/video/e3-2012-nintendo/731555
Official quote:
http://www.gametrailers.com/video/e3-2012-nintendo/731555
Official quote:
The new screen is not multitouch. Well, with the DS certainly it's not multitouch and people have really enjoyed that interface and have found it sufficient for their needs for gaming. If you add something like multitouch you do up the cost, and so we're trying to strike the right balance between the robust set of features and capablilites for the hardware but also make it affordable to people.