Yeah... seems we have yet another contradiction in the Core Rulebook.
Under Gunnery on page 183.
It specifically call out that you use Gunnery + Agility for manual operated vehicle weapons. And you use Gunnery + Logic for remote operated systems.
But under Control Device on page 238.
The first example for using the appropriate skill and attribute you would normally use is for firing a drone-mounted weapon. It specifically calls out using Gunnery + Agility.
Now, Fabe, I don't think anyone is suggesting you wouldn't use Pilot + Reaction to drive a vehicle. The discussion they are having is specifically about the fact that Gunnery switches between Agility and Logic. I don't think ClaytonCross was suggesting you use Logic for everything while operating remotely (just Gunnery).
Personally, I side with the idea that Gunnery + Logic while jumped in makes sense, because why does your physical hand-eye coordination have an effect on your ability to aim and shoot over the matrix? If the rigger's body is lying limp in the seat, why would the fact that he has Muscle Toner affect his ability to shoot the drone that he's jumped into?
Now, I had a bit of a hard time adjusting to the idea that you still use your Reaction for Piloting, because again, it didn't seem to make sense the your physical attributes would have an effect on your jumped-in abilities. I thought it would be similar to Astral attributes, where your Intuition (Mental reaction speed) would replace your physical twitch (Reaction). I came to terms with Reaction staying put for Piloting based on the idea that it could still be based on your neural impulses, which are increased by things like Wired Reflexes or Reaction enhancers. But I would still be stuck on the idea that your muscle tone has any effect on your ability to aim a remotely operated gun. The only explanation I can give for using Agility is if you are using a Virtual device (like AR through a Miracle Shooter) system to physically move and aim and have that input be what aims and shoots the remotely operated turret. So if someone is in AR and using Control Device to aim and shoot a remote-operate drone turret, I would let them opt to use Agility in that circumstance. But any sort of VR, it just doesn't really make sense to use Agility for any sort of tests... That would be like saying when the decker commands a robotic arm to lift a box, he needs to roll his Body+Strength to see if the arm can pick it up...