To be honest, I don't see any setup that doesn't use the mouse as a primary aiming tool as being especially effective. its simply so superior to other aiming devices that not using one puts you at a severe disadvantage. To that end I would personally recommend avoiding HOTAS (Hands on throttle and stick) setups unless you are trying to go for a real "sim" feel and are willing to accept the reduction in performance.
The setup I used for MW3 and 4, was a combination of a Saitek Cyborg gold and a mouse. The modern equivalent of the Cyborg Gold can be found here:
The stick can be configured for use in the left hand, and every element of its can be tweaked for optimal ergonomics. now, setting up the stick for optimal use in mechwarrior was a long road of trial and error, however by MW4 Black knight I had a system that was pretty effective. but essentially it boiled down to this:
The mouse is used for precision torso movement/aiming, with fire group 1 and 2 on the mouse 1 and 2, the Mouse 3 on the wheel was used for cycling targets and the mouses thumb button for jump jets.
Pushing the Joystick left and right turned the mech. Pushing the stick forward and backward does nothing. Twisting the stick gives fast torso twisting. The throttle is well, the throttle
now we come to the joystick buttons themselves, and this is where it gets complicated. IIRC the joystick trigger could be used as a "shift" button in MW4, allowing the top joystick buttons to server two function each. thus the top buttons gave me weapons groups 3, 4 and 5, as well as with the shift button pressed, reverse, zoom and override shutdown.
additionally the POV hat on the top of the joystick gives a fantastic sense of control, In MW4 the hat could be used to pull of "parthian" shots by swinging the arms out.
So as you can see, virtually all of the mission critical functions of a mech can be controlled directly with this setup, there were some more sophisticated functions that weren't easily available under this method, such as reverse target cycling, but everything that is necessary is available.
I am kind of hoping that this sort of setup will be come even more powerful in MWO, allowing for truly independent torso and arm control.
Anyway, i kind of rambled on, put the point is that you don't need to get an expensive peripheral to make the game more immersive AND be more competitive, a simple £30 joystick can work wonders.