If you only use the cross OR only use the L button, it's ok, it's not very comfortable but it's fine, but when you have to use both the cross, the L button and the touch screen it's awful. I can't play Metroid Prime Hunter because of that.
For me confort>efficiency, MPH über fast and precise but it's a pain to play, I have the same problem with PC games, keyboard+mouse is really efficient, but te keyword really isn't comfortable, it's so square and rigid, it looks like it wasn't design to be used with hands. That's the reason I prefer playing with a pad, stick aren't as precise as a mouth, there's much more button on the keyboard, so PC games can be more complex and more efficient, but it's not comfortable
I also don't like DS games that controls with the button but sometimes requires the touch screen in the middle of the gameplay, you have to grab the stylus and it completely ruin the feeling of the game.
The best remains stylus control with no buttons but that kinda limits the gameplay, which isn't such a bad thing for a handheld machine imo.