In other games, the PCs usually have some meaningful choices to make during combat. Who to attack, where to move, do they help a fellow PC or attack an NPC, etc., etc. In a game like Rogue Trader, Fantasy Flight's version at least, when you're in ship-to-ship combat most PCs don't have an opportunity to make any meaningful decisions. The Priest character could make a Put Your Backs Into It roll every round to inspire the crew, but it was the only way he could make any meaningful contribution during ship-to-ship encounters. It became very tedious very quickly. Though kudos to the design team for making sure everyone had something to do aboard ship.
You're absolutely right. Another problem is having these skills very often means the character is less skilled in areas that are likely more meaningful to them. In Fantasy Flight's Star Wars, being a hot shot pilot meant my skill tree was devoted to piloting but we spent the majority of the game on the ground.