Historically, FPS belong to PCs and KB+M. And historically, they have been designed around that kind of control, allowing for twitch-shooters given the quickness and precision that comes with mouse pointing.

On the other hand, it's perfectly possible to design an FPS from the ground up for analog controls. Case in exam: KZ2 or any other shooter that wants to give you heavy inertia in rotations, and moving away from the "camera on a stick" feel that comes with the quick, precise, abstract mouse controls.

Thus, I think that you should define what you mean with "better controls". If by better you mean easier, quicker, more precise at moving an aiming reticule across a view then obviously the mouse is better in that sense. Just like pointing with your eyesight would be even quicker, even more precise, even more abstract. And even worse at conveying weight, because it would basically allow for zero inertia of your body/weapon.

In the sense in which the controls, like the game mechanics, graphics, sounds, are trying to convey a peculiar feeling or experience, it all comes down to the game design. A properly designed game will make the best of any control method, and even bring out the unique positive points of it.

If I remember right Halo doesn't have auto-aim, at least it isn't obvious like it is in the COD series. Nothing like waiting for someone to walk by your crosshairs for it to automatically follow them(MW i'm looking at you) Does Halo have auto-aim?

You're quite correct.  In run and gun titles the accuracy and speed of response advantage outweighs running all the time, but for titles like Fallout 3 or Oblivion analogue movement is better.

I actually think the best control scheme for a pure shooter (i.e. nothing that needs to many buttons) would be something like the Wii Nunchuck for movement and strafing combined with a mouse for aim/shooting/melee.

Yes, Halo has auto-aim. 

Keyboard and Mouse cheating? ::chuckle:: I don't see how that can be when the controller and analog sticks is so much more natural and fluid for me. The Mouse and Keyboard are clunky to me. Of course that's personal preference. For me the controller is better. I don't believe either is 'Superior', that's kinda of a narrow view, but people have their preferences.

Honestly, I prefer controllers because I'm just better at it and it feels better.

Since I'm left handed I can never get the keyboard setup exactly how I want it, setting up the keys is always a pain, and I never remember how I do it from game to game so controls are always different from game to game.

It could be the little bit of auto aim most controller games put in, I don't know, but I just prefer to play the FPS with a controller.

PS3 has a mouse + analog control option (I think it came out for UT3), although I've never used it.

My only complaint about that, would be whether or not you have enough buttons (depending on the game, of course).

Neither is better. They are both better for their own reasons that cancel out. The skill level of the players is the same on either platform. As someone who played CoD4 extensively on both 360 and PC, I can attest to this. While the kb+m combo is much more accurate and easy to use for aiming, I still prefer the controller because I just think it feels more natural than using my left hand to press keys on a keyboard for movement. As to his argument about controllers being tougher, he is on the right track, he just didn't expand upon it very well, or you didn't include all of his arguments. Dual analog is much more difficult to use than a mouse for aiming. It requires much longer practice to master your sensitivity level. The unfortunate downside to this is that developers think they need to add auto-aim on consoles. I absolutely hate this feature because it is ALWAYS messing up my sniping on CoD4 when players are running in front of my aiming reticule.

Now, I'm not saying console players are more skilled because their input device is harder to master. The players on either game are equally skilled. I am the top player on either platform when I play, and I see no difference in skill level of others. If you take the best players on consoles, give them time to adapt to kb+m they will be just as good as the best players on PC and vice versa.

Oh, and just to try it out, I used a program called X-padder (I think) to map my 360 controller for CoD4 on PC, and while using the controller I was still in the top 3 players. The only problem with the controller was that when looking down the sights, there was no change in sensitivity like there is on console, so I was not used to that and it ruined it for me. If they could make a good "half" controller for the 360 that I could do movement with a controller and aiming with a mouse, I'd die a happy man.

I don't think it has excessive auto-aim, but I do feel it has slightly larger hit box/cross hair detection than a straight PC FPS.  I think any console FPS has to be slightly more generous in what it counts as a hit.  Typically the movement in console FPS is slower to align to the controls better, while pure PC FPS allow faster movement due to the speed with which you can aim.  I'm not sure if it's a good average, but I seem to remember Unreal Tournament 3 on PS3/360 had around 20% slower movement speed.

I don't think I'm going to convince you, but there's no reason being left-handed should be a hindrance.  You could place your right hand on IKJL keys for movement (with your index finger on the 'J' key, just like when you type) and your left hand on the mouse.