On the topic of boarding: Completely destroying a ship is much easier than boarding, of course, and it's difficult to make a ship "boardable" without sucking out the air through a vacuum or making it explode. Here's the reason why it should be prominent: Back in the old days of sea-faring vessels, the goal when firing upon an enemy was NOT to sink him, because if you did that, then all the valuable cargo onboard would be lost. It's the same thing here: If you completely destroy a ship, you can't take prisoners to interrogate, you'll probably lose most of, if not all of the valuable cargo, and there will be much less to salvage in general. If you successfully board it, however, you can salvage the ship, take prisoners, and retrieve anything valuable onboard.
On the topic of the role of NPC's: Firstly, you cannot assume that all ship systems will be able to be controlled by a single person. When you have a 1km+ ship with thousands of turrets per side, and you're being swarmed by hundreds of enemy fighters, you can't possibly hope to aim all of those guns by yourself. Hence, NPC gunners, or at least a very complicated A.I. Also, repair nanites are great, but what if you can't affor them? Maybe they're a lot more expensive, and you have a relatively small ship that's still big enough that you can't repair it yourself. maybe in some cases, like this one, a small team of NPC's is less expensive than repair nanites. Of course, the cutting-edge, fancy, expensive vessels probably have fully automated systems, with repair nanites and self-aiming turrets, or even a mass turret-control interface, but what if you have a VERY fancy ship that can split itself into a bunch of smaller ships, or even just a big ol' honker that depends on fighters for versatile offense? Who's going to be piloting everything you aren't going to be? If you don't have one of those fancy mass ship-control systems, you'd better hope you have enough pilots for all that. What about ground offense? Don't you want a few squads to send onto a planet to go scouting, or go kill people? How about the boarding party? Maybe you're a fighter pilot. Who's controlling your rear turret? Surely you can't focus on all those flips and rolls AND shooting the main cannons, and aim your rear turret too? Sure, you could just have an A.I. do it, but what if you (or your captain) can't afford it? You'll prolly want a gunner, right? Exactly. And even if all that's automated, who's in charge of the medical bay? Who's looking over hydroponics? Who's maintaining the reactor levels, repairing the fighters, serving food, researching new technology, interrogating the prisoners, guarding the prisoners, executing the prisoners, being the prisoners, or even swabbing the deck? And if all that is automated, then good luck staying sane, Mr. My-ship-is-entirely-automated McLonelypants.