For the time being, fighters are on the back burner (excuse the pun!)
As for shuttles, basic proficiency needs to be all the operation of the console – pitching up, down, rolling left and right, yaw (or whichever controls are included), stopping, boosting and docking. There also needs to be a basic exercise like depart the ship, collect a life pod and return. Navigation could be made more difficult by placing the lifepod in an asteroid field. There doesn’t necessarily need to be any firing involved as that isn’t what the shuttle will be used for, though a very basic exercise could be shooting down drones launched from a Kralien drone cruiser if we think there should be a small element of combat.
As for fighters, basic proficiency would be as the shuttle, just with an expansion on the combat side. Infact, shuttle proficiency could be the first step, with fighter proficiency being one level up. Things like target identification/ attacking a specific target (drones or ships, kraliens or torgoths, W83 or R54 etc), evasion and some kind of coordination with ships or other fighters.