I think some people can get some use out of my control setup for an Xbox 360 pad/PS3 controller (with SCP's DS3 tool).

Features:

• D-pad + Ⓐ sharp/incremental aim for precision sniping
• Walking with the d-pad for sneaky stealth ops
• Crouching with Ⓧ
• Jetpacking/jumping with Ⓑ (as well as L-stick up)
• Grapple gun retract using L-stick up + Ⓧ
• D-pad can navigate Trade-Star buy menu

There are two versions attached. The one I use has the bumpers and triggers swapped compared to the built in 360 preset. I use PS3 controllers so I try to avoid the triggers. The other one uses the right trigger to fire as is standard.

To clarify the controls:
A = sharp aim
B = jetpack/jump
X = crouch
D-Pad Left/Right = walk left/right
D-Pad Up/Down = increment aim up/down
R-Stick = walk/jetpack/crouch
L-stick = aim

Updated for B32 to include reloading with Y and switching weapons with clicking the sticks.