Man, this is a tough question for me. I guess if I had to pick a DS game I'd say Hotel Dusk. My expectations weren't high and it was pretty tough to get into, but once I did, boy what a ride that was.
I can agree with Lux-Pain though. Usually story based games get much better as you get into them, but that just never went anywhere. The fights were starting to get kinda cool but I just got way too bored.