Don't try to pinpoint all your shots (at least not until we get Analog Turning). Lead your target and let them walk into your triggering point.
The "C" command is your friend. Keep it handy because it will instantly allign all reticles and your torso and if you try to do this manually with a Joystick it can take you out of the fight for 3 to 5 seconds.
Set your Joystick up with large Deadzones so you are only activating the axii you want. MWO's pitch, torso-twist, and turning are all independent of each other, but can trigger accidently if the deadzones are too small.
One more thing. Until we get Analog Turning, the way to make a very accurate shot with your Joystick is to replace the Turn with a Torso Twist for you final allignment. If your twist and pitch sensitivity is adjusted correctly you will actually have as much control as a Mouse gives you, but not quite the tracking speed. We do have Analog Twist and Pitch already.
If your Joystick doesn't have a Profiler or it's not very good you can use the User.cfg file in your
C:\Games\Piranha Games\MechWarrior Online folder. And here is what that looks like
cl_joystick_gain = 6 cl_joystick_sensitivity = 1 cl_joystick_throttle_range = 0 cl_joystick_invert_throttle = 1 cl_joystick_invert_pitch = 1 cl_joystick_invert_yaw = 0 cl_joystick_invert_turn = 0 cl_joystick_deadzone = 0.1