If you wish to use a joystick or gamepad with Ghost Recon, you can only do so if your Joystick / Gamepad has software that allows you to assign keyboard strokes to movement and buttons. Contact your controller manufacturer or the documentation that came with the controller to see if you have the ability to assign keystokes to movement and buttons.
This is possible through the use of the controller software and not through Ghost Recon.
For example, if you have one of Microsoft's Sidewinder line of controllers, you can use the Sidewinder software to assign keystrokes in the following manner:
You remap the keys on your joystick in the games remap keys section of the options screen. In remap keys section, select the action you wish to assign a button to, click on this action with the mouse, then hit the button to which you want to assign an action.
If your joystick includes software to map keys to the buttons and directional pad or Joystick movement, this is most likely the best option. NOTE: before trying this, check your joystick / gamepad documentation to ensure your controller has this ability to assign keystorkes to movement and that you are able to change these configurations.
Using this software, assign keystrokes to the directional pad or joystick. Once in Ghost Recon, you should leave all joystick options off. Ghost Recon should continue to think you are using a keyboard.
Using the example of Microsoft's Sidewinder software, the following illustrates the possibility of configuring a controller in this manner:
Use the software that came with the Sidewinder to create a new profile for Ghost Recon. Read the help file included with the Sidewinder software for help with assigning keystrokes to movement and creating new profiles. For example, you should be able to assign w to forward movement, w+a to left diagonal movement, a to left movement and so on. It is important not to leave out diagonal movement when assigning keystrokes in this manner. Button assignments can either be made here, or in the game's remap keys section.