Agree with previous suggestions 🙂 the PD is a prime candidate for going offline with no control rooms of any size.
I like the build grid size idea, but lends itself to upgrade costs, progression, and 'tech level' prereq's for more parts. eg., could you build a "large" CR w/o a "small" one present first? Require use of all size types, by linking to 'command points' or abilities.
Perhaps a 'small' room is necessary to command small weapons. A 'large' room specializes in large weapons. (And perhaps advanced gear like shields.) So you would need both on a ship to use both types. But additionally the large room enables larger grid sizes and crews.
Related, I like the idea of control rooms unlocking the use of certain parts anywhere, such as shields, but not requiring the shield be in range of a CR. Weapons yes, but perhaps not defensive parts.
You will want to rebuild CR's asap to regain use of the weapon types in their range that they can control. A 'large' should be expensive, and may lead to cost-control tradeoffs if a player has built it too early.
I don't think the CR needs to limit part count, that's also limited by grid size, needing more CR's, which themselves take up space. A 'large' should enable more grid space and crews than a 'small' version, therefore be a more efficient choice than having a bunch of small CR's.
Making the control room the lynch pin to knocking sections of the ship offline, might become an alternate primary target compared to Reactors, which cause massive collateral damage.
Trying to surgically knock out an enemy ship, ties into the resources and salvage plan. Quite a few stock ships have reactor weak spots that vaporize most of the ship when they explode. I hadn't even considered control rooms: destroying or disabling (unpowered or uncrewed) all CR's on a ship, would be a good method to add as a new win condition for bounty hunter mode.