As a gamer who's bought into the pseudo-fourth generation Nintendo DS (Not counting DSiXL...that's just a DS with steroids), it's a little odd for me to say that I'm comfortable NOT putting a screen protector on the bottom screen. After so many iterations, Nintendo seems to have done it right this time around.
I want to really chalk it up to me being lazy for getting one in the first place, and I'm typically uber-OCD when it comes to scratches on my screens. But the new touch screen has endured many fingerprints and stylus, enough for me to almost never purchase a screen protector again.
For a good week now, all I've used is a microcloth to buff out fingerprints and hardened stains, and the screens remain spotless. The hardware is proving to be quite reliable in endurance, and now only its heavy price-point is what will drive me to add the extra protection.
And, for the record, I only apply screen protectors on the touch screen. Unless you have people that will insist on touching the top screen because they believe both are touch-sensitive, I don't even bother with the top screen.