I would want joystick support because many people (like me) play various FPSs with a joystick, having to convert to a keyboard would make things complicated.
And also, If you do, don't make it exactly like the Quake II joystick source code. It has bad compatibility (ie I don't play it anymore because it doesn't support my SNES Pad).
I think it's possible to configure most decent joysticks to work with Q2W. Jester plays with a joystick. That said, I have no intention of working on this myself, but I've created a Trac ticket in case someone else wants to add support for cheaper joysticks: http://jdolan.dyndns.org/trac/ticket/135