I prefer d-pad controls more. Personally, I'm so used to playing with them. Last year was the first time I bought a DS. I guess its kinda a drag to have to pull out that stylus all the time, and I lose mine really easy. It's a nice innovation, like it makes it so much easier if I'm playing something like Trauma Center, but some games are easy enough to play without the use of the stylus. I've been playing a lot of Phoenix Wright lately, and it's so easy to use the D-pad to select what I want, the L button to press the witness, and the R button to access the court record in play. And if I'm playing a real casual game like that, without fast paced action, I sometimes use my thumb instead of the stylus to navigate the touch screen. I know you aren't really supposed to but I don't care. I'll just take an eyeglass cloth and wipe off my screen.
EDIT: Oh, I forgot. That's most cases. I forgot about Picross. It's easier to touch the block than to make my selector go all over it since I'm very random with my logic. I guess it depends on the game, but Im more of a d-pad fan. Oh, and btw, sometimes the stylus isn't as accurate as I like it to be. For me, the reactiveness depends on which angle I'm holding my stylus at. Sometimes I'll try to draw a line in WarioWare Touched! or maybe a picture in Drawn To Life, and it's kinda hard sometimes. And I have not put on my American Hori slightly cheaper quality screen protector just yet.