Let's see if I can throw a loophole into just about every Starfleet overlay ...
Anyone else thinking that Vehicle Operation (Shuttlecraft) would be better served by using Shipbard System (Flight Control) ?
Shuttles basically have all the same characteristics as any other ship. Warp drive, weapons, sensors etc etc etc ...
Every Starfleet character has some rating in Shipboard Systems so could pilot and work the systems on a shuttle with that skill regardless of whether they have the (Flight Control) specialty for piloting ...
Seems a little unnecessary to me ...
The loophole then becomes replacing every overlay with something in its place ... especially the odd one that have it at 2 (3) level ...
Still pondering new skills from other sources and such and a whole new way of doing Starfleet overlays and advanced training to replace the whole "command" as a branch right from the get go. So this skill was one of the ones that had me wondering about its value ...
Even the Fighter Pilot overlay in the DWS uses Shipboard Systems and the fighter's are no bigger than the shuttles. It makes sense to me that that's how it should be as you need a crew to work all the systems, otherwise you would think it would all be covered under Vehicle Operation (Fighters) as shuttles are, but that overlay has Vehicle Operation (Armored Assault Craft or other aircraft).
So I'd see Vehicle Operation covering the non-warp capable atmospheric craft, workbees etc & land/water/air vehicles.