Have you ever tried to envision a 22-man emergency transporter room? How about an airlock/docking port? Any science labs or weapons stations? Or maybe the ship's brig/security area/armory?
I plan on adding many areas not seen on the show, including all of the ones you've listed. Some other areas I'm planning are:
Main cargo bay w/ cargo transporters
Officer's Lounge (with a bar, similar to Ten Forward)
And perhaps a ready room / office for Kirk (which will be a redress of Pike's cabin seen in "The Cage"