yeah, the type of fps games change to better suit the systems. You compare FPS games on the N64 to what was out on the PC and they played very different; slower paced and crazy amounts of auto-aim. Even after the PS1 had dual analog as a standard control scheme, Halo was the game that kinda defined dual analog shooters with the sticky aim and acceleration trickery. Now there is the CoD approach where they have two sensitivities, one when aiming and one when just looking around, not to forget the little nudge when you pull on that aim button. When people talk about how some games feel like PC games or console games, it isn't just a bunch of nonsense.
I'd say we haven't really seen that a defining pointer or touch screen shooter yet. I still think a touch screen is the best solution for a "second stick" that would actually be an improvement in the long run, at least if they let you use your thumb comfortably like the ipod touch.
and it's not just shooters, it's basic camera control for 3D games. Assuming the 3DS is gamecube quality, they need some camera solution. Ideally we could just say "they'll find a way without the player managing the camera" that won't happen.