4 for control surfaces (throttle, elevator, rudder, aerolons)
2 for pan/tilt
perhaps 1 for your autopilot/flight stabilizer
Check out Channel Wizard http://www.rcgroups.com/forums/showthread.php?t=1576877 for ways of extending a cheap 6 channel effectively.
I think RC radios on UAVs are probably going the way of the buggy whip pretty soon. I lost mine and I'm not planning to get another. I've got a USB RC-style controller (RC flight sim style) and a microsoft sidewinder 3d, so I don't see any reason to waste the money, weight, and RF power on an oldskool controller.
Jake, is that system something you crafted or a purchased system? I would sure be interested in something like that if its available
Paparazzi GCS supports using a joystick. Mission planner looks like it does too.
I use a USB RC-style controller like this...
It works just fine. It plugs in and shows up just like a regular joystick. If you want to fly with one hand and have a ton of channels I suggest a MS Sidewinder 3D or other 3D joystick. On 3D joysticks the shaft also twists for rudder control. Most also have a throttle and a hat switch on top (use for camera control).
With a setup like that you can control everything with one hand and use the computer with the other.
If you're going to use a laptop in the field there's no point in not running everything through it. The computer will do the control, video, OSD, etc..
We are discussing transmitters to fly an actual RC aircraft right? Not flight simulator flight? I'd recommend getting at least a 7 channel 2.4ghz radio. A 9 channel would be really sweet and the more the merrier I would say. If you are doing FPV or aerial imaging you may want two radios, one for flight and the other to control the camera. (Camera operator should not be flying the plane of course.)
Why not control it through the computer? Why spend all the extra money on electronics that duplicate stuff your computer already does just to use a crappier radio than your data link.
Why spam out all that extra radio noise also? It's a shared and crowded spectrum so why do you think you should use 2 radio links for one drone? If there's any interference problems you'll be the first one that's shut down and kicked off the field.