There are two issues which mean that the Wii Controller is not an ideal solution as a gun, although seems adequate for many people.
The first is that it was never designed to be a calibrated device, as the Wii pointer just roughly moves in the direction of the controller, it does not follow the controller exactly.
This can be partly overcome by drivers which have some kind of calibration built in, so it can be calibrated in such as way that when the gun is lined up, the pointer follows it.
Then this leads onto the second problem. In the Wii setup, the pointer moves further than the relative movement of the controller. This means its easy to ensure the sensor in the remote can always see the IR LEDs, beacuse the movement of the controller is quite small, the LEDs are always in the field of view.
In a calibrated setup, the controller needs to move further, in fact it needs to be physically pointed at the corners of the screen, at worst case. This means it would lose sight of the LEDs, unless the controller is located a good distance away from the screen. Most people prefer the gun to be quite close to the screen, so this makes this problem even more difficult to overcome.