Re: NX class ship - what would you change?
That's a pretty big space, but you don't have to replace it with another large room. It could be subdivided into some of or a mixture of these:
Auxiliary Technobabble Access.
Or even a dog park.
Edit: I'm assuming you meant the engine room, but then you say the transporter is out. So you want to replace that alcove it sits in?
Dr. Howard, Dr. Fine, Dr. Howard: For Duty and Humanity!
--Men in Black, 1934.