(Sorry for all the suggestions, guys. I've been traveling so I had a lot of time to think.)
It would be nice if you could designate a part of the ship as it's own. Technically, it's the same vessel, but the area selected would be cut off-however, you could choose to keep the shielding and you could link weapons from other parts of the ship. This wouldn't affect current builds, as it would be completely optional. This way, you could design separate power designs for a certain weapon or engine, or have people/AI run around and zap things with power pistols.
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tl;dr: Giving parts of the ship it's own power, while allowing it to keep shielding and part of your ships weapon systems
It would be nice if you could designate a part of the ship as it's own. Technically, it's the same vessel, but the area selected would be cut off-however, you could choose to keep the shielding and you could link weapons from other parts of the ship. This wouldn't affect current builds, as it would be completely optional. This way, you could design separate power designs for a certain weapon or engine, or have people/AI run around and zap things with power pistols.
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tl;dr: Giving parts of the ship it's own power, while allowing it to keep shielding and part of your ships weapon systems