Some troopers arent that bad who get mind-controlled. The more they get panicked by aliens the more their bravery increases. Also you can have really good troopers who are psi-weaklings, ive got an awesome sniper but he always gets targeted first.
Handy solution, dont use those psi-weak soldiers against sectoids or etherials, when you have the Hyperwave Decoder if the enemy is not a sectoid or etherial then you can use your psi-weak troopers, either have a dedicated craft of psi-weaklings or just manually substitute troopers on a craft once you know who the enemy is.
The control room in an alien base is the metallic structure which is on the brown floor, all other metallic structures will be on the mettallic floor so it should be easy to spot, not to mention it is fairly large, the actual control room is on the 2nd floor and usually has a blaster-bomb wielding alien.
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