Both Mario and Metroid both include a few different ways to control, so it loks promising that future games will let you choose. I find that the thumbs-strap in "touch mode" is by far the best way to control Mario since it closley mimicks an analog stick. The D-Pad worked fine for a while, but eventually it became too cluncky and I had to switch. Using dual-touch mode with the stylus is impossible to play, in my opinion.
For metroid, the first control scheme is perfect with the stylus. DON'T CHANGE IT.
I'm not too keen on using my DS for playing GBA games though. I mean, the screen is bitchin (what) and all, but it's too hard to control fast action games (for slow paced stuff like RPG's or Strategies it's fine). I have a hard time playing Metroid Fusion because I always want to use X as my B-button, since it's positioned in relation to A like it was on my SP. Also, the D-Pad is VERY sensitive and frustrating at times. Try playing the Fly-swatter game in Wario Ware.
I'd like to see an Ikaruga-type game in the DS becasue the screens are set up perfectly for one (can't think of a use for the touch screen...but wireless co-op mode would work), but I'm afraid that if the game requires incredible amounts of precision on the fly, like Ikaruga, it'd be way too hard to control.
Oh, is anyone else's A button just a wee bit lower than the other face buttons?