The current implementation of these abilites can not possibly be working as intended. These abilities were intended for ship classes, not captain classes. There was some sort of "reasoning" that "modular ship design" allowed for subnucs in escorts, and cruisers dancing to attack patterns. It makes PVP silly! Tee Hee!
That is garbage. Truly and simply garbage.
Remove those abilites from captains and bake them into the ship classes where they belong. Done. Get past it.
This is essentially the same pattern that Boffs follow.
Or split it up. Bake some into the ship, but allow for a captains chair station and allow certain abilites (not all) but some to be chosen in that manner. Seems a bit advanced to me, I think just baking them into the ships for now would be far more predictable. And that's good for balance.
All of what will be called Ship Class abilities will need to be skilled by the player if they wish to be super good at it. You don't spend skill points in sciency magic? Well hopping into a Science ship to use sub nuc won't be working out that well for you. It will WORK, just not as well as someone that skills for it. Oh thats right. Previously you didn't need to spend skill points. Now you will.
Captains are already free to spend points as they wish. Make it so ALL the points they spend have meaning vs the abilities and ships they intend to use. There can no longer be FREE abilities. The Previous costs for owning those abilites has been REMOVED and it needs to go BACK IN but in a manner that doensn't punish the player or LOCK them into a single path.
This will be an additional way to allow for greater design leeway. Ships could have much greater variety than they do now without fretting over the huge issues that mixing "captain abilities" and "ship classes" brought to the game.
And it allows for truly hybrid class ships. How about a fast attack craft with just Alpha AND Sub nuc, but NO other ability. How about a Massive cruiser with scattering field, team eps 5k, and um...something else! This would be a GREAT way and opportunity to address the engineering ships.