Will FPS's use the back touchscreen as left and right trigger, so it feels more like you are holding a controller. I haven't felt the Vita or played a FPS on one obviously but it seems like it would feel awkward holding it so you can use both analog sticks and left and right shoulder buttons.
After messing around with a co-worker's Vita for a few minutes last week, I think it's incredibly comfortable holding the device, accessing the analog sticks with your thumbs, and using the Left and Right buttons.
I played ModNation Racers, which uses the L and R buttons for braking and accelerating. It felt really good and natural. I have fairly small hands, however.
I'd imagine third and first person shooters would feel really good. The front touch screen could possibly be used for functions that are generally put on the L2 and R2 buttons. The rear pad as well.
From what I see in most shooters, the L2 and R2 buttons are used for either throwing grenades and sprinting. To be honest, I think just a tap of the back pad on the left or right side could easily serve those purposes. We'll see, what with Resistance and CoD hitting the Vita this year.