IMHO, Bk2 and Bk5 ship rules represent two distinct scenarions.
In Bk2 rules, ships being small, the skill of the crew is greatly featured, with most skills being useful in starshp operations and combat (as long as the computers allow you to run programs that make those skills useful). If you run a maeover/evde program, the skill of the Pilot is the key. If you run a Gunner Interact, the skill of the gunner is the key.
In Bk5, OTOH, ships are assumed to be larger, with their crews in the order of thens to thousends of people, whose skills are not so featured and the ship's performance are more vital than the crew's skills. Only Pilot and Ship's tactics have a ture effect in ship combat, and the most vital aspect are the computer rating (assuming, I guess, better programs capacity and ECM) and agility.
To try to reconcile both of them, one must either use the Bk2 rules in larger ships (something unpractical for the sheer number of firings) or to use Bk5 rules in smaller ships (akin that done in MT with ship design/combat), so reducing the crew skills to nearly useless (except those told above), and so, IMHO gain, downplaying the characters role (and so roleplaying).