I prefer the wii controller now for all FPS and 3rdPS. I played both call of Duty 4 and Orange Box on analog pads after I played Metroid 3, RE:4 and MoHH2 and I had a hard time adjusting. eventually I bought orange box for PC because I just didn't like the controls as well as mouse and keyboard.
As much as i am looking forward to RE:5 i really wish it had IR control.