Morrowind on the PC was not designed to use a gamepad. You need something like Xpadder. I also seem to remember that third party gamepads had better success on the PC version of the game.
But, you will lose your hotkeys, and the HUD on the PC is really designed for the keyboard and mouse. Also, you can resize all the menus, move them around, and pick and choose which ones you see when you right click.
Here is someone that got the 360 controller to work
http://forums.nexusmods.com/index.php?/topic/171416-how-to-use-a-xbox-360-gamepad-for-morrowind-pc/