Yes, it can be quite annoying to do any sort of precise aiming on a console (Manhunt 2 on PS2 comes to mind). I feel FPSs pretty much shifted to the consoles in the X360/PS3 gen. I guess Halo and Modern Warfare are two of the main reasons, since they have been so successful in consoles.
Despite a mouse being awesome though, I have no problem playing well on a N64 (GoldenEye, Perfect Dark). The Z trigger is a delight. Might be that I'm just too used to the controller, tough. With a GC controller on the other hand, even though it's pretty much the most comfortable thing I've ever hold, aiming with the C stick is very hard for me (at least on Time Splitters 2); it has too much dead zone and once past the dead zone it's just too sensitive.
And while it is somewhat a matter of getting familiar with the controls, I will say the Playstation controller is very inferior to the Xbox one when it comes FPS. The asymmetrical sticks on the Xbox gives it a much more natural handle.