StingingVelvet: One could argue playing games how they were designed is always the best way, but getting over 20 years of mouse aim use isn't the easiest thing. I feel drunk when I play first-person games with a pad.
I'm not fully sure it is only about what you're used to (if that is what you were suggesting). I always played e.g. Doom 1-2 with only keyboard, I didn't feel mouse offered any big benefit in them.
I started playing Duke3D the same way, but at some point I decided to give the mouselook a try. Duke3D is officially the first (FPS) game for me where I used mouse aiming. And I feel I got it instantly, it felt very easy and natural from the start, something that gamepad FPS has never felt to me even after prolonged PS2 (or even PSX) FPS sessions. Hence, I am pretty sure I'd probably feel the same even if I had ever played only console FPS before with gamepads.
It is a bit like I do have to rely on the touchpad on my laptop quite often (not for gaming, but desktop work). I can get used to it, but it always just feels much inferior to using a mouse. Don't get me started on those tiny rubber thumbsticks on some laptops, I've always hated them with a passion...
I've also seen one kid, which was pretty much console gaming kid only, to pick up the WASD+mouse controls quite fast when he started playing Minecraft on PC. He wasn't really gaming on PC before that, yet he seemed to master the kb+mouse setup quite fast.