Yes, BF3 it planned to have joystick support on PC. You could not remap controls at all in beta.
As someone whos played battlefield games since 64 player bf1942 in the year 2002, a joystick is the best way to own with jets. Even a 360 gamepad does not come close to the precision a joystick provides. It is also much easier to transition from joystick and keyboard to mouse and keyboard for infantry than it is to pick up a gamepad with two hands. People can get pretty good with a gamepad or even a mouse, but most of the very best have joysticks.
Bad Company is not a good comparison since it does not have jets and 64 players.
Edit - This thread is only directed at people who care about being really competitive. Also, you don't need to spend a ton of money. You can get a decent one for under $40, which is less than a 360 gamepad.