As far as the pilot thing goes, the pre-req was pretty much laid down in the AD rules even before KH was published. The Operate Machinery subskill of technicians says that you need to be LVL:2 to pilot jetcopters, LVL:4 for air cars, and LVL:6 for shuttles. Hence the LVL:6 tech background for a ship pilot, as that's the next progression (system ships, small starships, etc w/ each pilot level).

Astrogators need a healthy background in program manipulation and displaying of information (hence the high computer pre-req). Gunners need a healthy background in trajectory, and the closest thing to that is the corresponding weapon skills. I always felt that in addition to robotics, an engineer should hae a working knowledge of computers as well...such as LVL:1 robotics and LVL:1 computer

Perhaps it is this flaw of the AD skill system...that only certain SUBSKILLS are mandated. This may have been one ideal behind the Zebulon Guide splitting up of skills, perhaps their planned future editions were going to cover ship skills with a mere high level Operate Machinery as a pre-req rather than having all the technical skills at a high level. It was something I was experimenting with as well...allowing a character to buy all the subskills at 0 level and improve them individually (at a lower XP expenditure) rather than as a whole. That way one technician would be an accomplished operator, another an accomplished repairman, a third could be an accomplished security systems man, etc