I think the regular controls are great, especially when using some kind of extra support (including the stand). BUT after trying out the old DS thumb stylus, it is now my preferred control method. I sometimes have trouble with it's aiming precision in the on-foot sections, but the trade off is having better control over Pit's movement/ shooting. I don't remember how I played through Metroid Prime Hunters, but I'm assuming it was with the thumb stylus. I suggest it to anyone who wants more comfortable/ natural touch screen controls.
Note if you have short thumbs this method may not work well for you!