I think there may be three roles here that are being lumped into two for the pilot/captain, but at the same time this is largely going to reiterate what Hamster said:
-ability to work the ship into a good position for its gunners, and out of a bad position from the opposite team's gunners (strictly pilot)
-ability to work with the other ships on the team (captain, and probably should be pilot too)
-ability to direct the crew
now, if the pilot/captain can manage all of that, that truly makes a great one. but that is a lot to handle.
I realize this isn't going to work in most cases, but when my fiance's piloting/captaining a pyra, I'll play either gunner or gungineer on the top deck, and act as his "First Mate" - I'll keep an eye on the crew and the components that're getting damaged, and I'll direct the crew for him, and keep people on their stations. it has worked pretty well for us so far.
so on a related note, I'm going to add to this: there's something yet to be mentioned here, and that's what makes a great crew. for some, it's realizing when direction is needed, and knowing enough about all the different jobs and what works effectively on the ship you're on (in short, experience), and to be able to dispense that knowledge (without being a jerk about it). for others, it's going to be how they handle the direction they're given, or otherwise knowing when to request direction for themselves or other members of the crew, and when to ask for help from other crew members.
and then there's above and beyond, when a crew member understands the ship and their role on it and kicks butt at it so well that if they need any direction, it's very limited. generally, you get a crew that understands their role well, whether instinctually or by direction, that's what wins matches.
now, a second for gunner. I had a really awesome match as gunner recently, and a couple of terrible matches today, and I've been going over what worked and what didn't. it seems largely that the matches that don't go well are the ones in which the crew doesn't have as good direction. in one of those terrible matches, an engineer manned the only gun that's pointed at an enemy as I approached it, and I'm left standing around and repairing the hull as it needs it (a job they could do way more effectively if they have the right equipment), meanwhile the ammo I had loaded into that gun is being cleared. as a crew, we suffered from lack of direction; the engineer and I both thought we needed to be in the same place at the same time, and we ended up role-swapping...which may be okay in some circumstances, but well, we did meet our demise, and I firmly believe that was the reason. that really awesome match, we each knew our role and our stations. so, the larger part in my experience is exactly what I typed out above. it is absolutely key.
there is more to being gunner than that: knowing the guns of the ship you're on and what ammo is effective in them, both short-range and long, and having a strategy to fixing your gun when the rest of the crew is busy on the hull, balloon and engines (because guns are probably going to be last priority to keeping the ship afloat, from an engineer's perspective - and even if it's not, if you can effectively put out a fire and/or repair your gun while reloading as a gunner, that's one less thing they have to worry about). remembering to reload your weapon at that moment when there's a break in battle or when ships are moving just so that you can't hit anything (and realizing how quickly they'll be back in range; whether or not reloading right then would be a good idea). that last one is so little, so easily forgotten, and under most circumstances, it won't matter...but in what few matches it does, it'll separate out an excellent gunner from a good gunner.
engineer: have a beaten the dead horse enough yet? otherwise, knowing your station (if there are stations), and being able to prioritize that station (or the whole ship), and having a strategy to help the other engineers or ask for help from them.
and then there's...knowing when you're an engineer or a gungineer. in most matches I've played, when the action hit, at least one engineer was too busy keeping the hull up and running around like a chicken with its head cut off trying to manage the rest of the ship components to ever think about touching a gun. sometimes, you're an engineer. sometimes, you're a gungineer - on a gun until something within the gungingeer's station starts breaking or until the dedicated engineer needs help. knowing which is needed, when to be on a gun and when to be on repairs will make or break the battle.
