One thing I can’t understand in Rogue Trader (or Dark Heresy) is why fighting skills are talent and not, well, skills.

You use Weapon Skill or Ballistic Skill for every combat action, with a malus if you don’t have a talent, and modificators. That’s it. No skill.
Let’s say you have the Pistol(universal) and Basic(universal). The only weapons you want to train with are plasma pistol and boltgun.
It doesn’t matter if you have spend countless hours to shoot plasma charges. It’s nothing to have shot billions of bolts, or missiles, or whatever. You have exactly the same skills with a lasgun or your boltgun. You shoot just as well with an hand-cannon and your plasma gun.
You can’t be a specialist.

Well, let’s add some new skills :

Advanced (choose one) weapon training (choose one) +10 cost 200
Perfect (choose one) weapon training (choose one) +20 cost 200

Exemple : Pistol Weapon training (Universal) cost 500
Advanced Pistol weapon training (plasma) +10 cost 200
Perfect Pistol weapon training (plasma) +20 cost 200

Without the first, you have -20 to BS when shooting your plasma gun and every other pistol.
With the first you use BS with your plasma gun, and every other pistol.
With Advanced, you use BS + 10 with your plasma gun, and BS with other pistol.
With Perfect, you use BS + 20 with your plasma gun and BS with other pistol.

It’s not rocket science, but it’s on par with the other skills. Keep track on when Advanced and Perfect should be available for players. Of course it will be some ranks AFTER the first skill. How much ranks depend on the career you choose.

Exemple : Arch-militant : Pistol Weapon training (Universal) rank 1
Advanced Pistol weapon training (plasma) +10 rank 2
Perfect Pistol weapon training (plasma) +20 rank 3
Exactly like Dodge, the arch-militant gain training very quickly, every rank after the first..

Astropath : Pistol Weapon training (Universal) rank 1
Advanced Pistol weapon training (plasma) +10 rank 5
Perfect Pistol weapon training (plasma) +20 never
Basic weapon training (Universal) rank 6
Adv. Basic weapon training (bolt) +10 never
Not so good with a gun, it take 4 ranks to advance for the psyker. So he will never be better than average with a boltgun.

IMO, this doesn't change the balance of the game, and that make fighters better fighters. Of course the arch-militant with Expert Ballistic and Perfect Basic weapon training (Boltgun) will have something like 40% more chance to hit than a astropath with the same boltgun. Add to this the talents of the arch-militant, and you will have an even bigger difference.

But when the boltgun are empty, and all they have left is a stock of standart Imperial Guard lasgun, there is not so much difference anymore. And a rank 8 arch-militant should be a better shooter than a rank 8 astropath, anyway.

And what about spaceships shooting at each other? No skill for that? Only Ballistic Skill? So an arch-militant is as good than a void-master at calculating battery solutions? I don't think so.

Enter the Gunnery Training (choose one), and Advanced and Perfect Gunnery training.
Gunnery training (macrobattery) or (lance) or (torpedo) : 100 (each) rank 1 for Void-master, rank 3 for rogue trader, rank 6 for navigator
Advanced Gunnery training (choose one) : cost 200 rank 3 for void master, rank 6 for rogue trader, navigator never
Perfect Gunnery training (choose one) : cost 200 rank 5 for void master, rogue trader never, navigator never.

Of course, a character without training will use BS -20. Good luck with that.

A character can use his skill when shooting one type of weapon per turn, and only in one direction.

Example:
The havok raider "Killing Joke" is attacking a merchant ship. The void master is trained in Gunnery (macrobattery), Gunnery (Lance), and also in Advanced Gunnery (Lance). The rogue traider, captain of the "Killing joke" is trained in Gunnery (macrobattery). The rogue traider will make a Ballistic Skill roll for the dorsal battery, and his Void-master will make a BS +10 roll with the lance weapon.

The Lunar-class cruiser "Lord Daros" is fighting an ork kroozer. The void master is trained in Gunnery (macrobattery), Gunnery (Lance), Advanced Gunnery (macrobattery), Advanced Gunnery (Lance) and Perfect Gunnery (macrobattery) and Perfect Gunnery (Lance). Yes, he is quit good at his work. The captain of the ship is trained in Gunnery and Advanced Gunnery (Lance). the void-master will roll BS +20 for the two starboard batteries, in one or two salvo. The captain will use the front lance battery at BS +10.
If they want to shoot with the port batteries (on something else, of course), they have to use the skill of another character ("Wake up this **** navigator, for Terra!") or use the skill of the crew.

The crew :

Incompetent crew are not trained in using their guns. But they are so bad, they can hope for some beginner’s luck. Roll with BS 20.

Competent crew are just that, competent. They have the gunnery training of the guns they are using. Roll with BS 30.

Crack crew are well trained. They have an advanced training in the gun they use. Roll BS 40 + 10

Veteran crew are the best out there. They have an advanced training in the gun they use. Roll BS 50 + 10. Yes, that's probably better than the shooting skill of the captain, so a good captain will use the skills of his crew, and do something else than grunt work.