How about Spock having his own damn Science area!
Okay, no science officer has ever had their own section, but it might have been cool to have Spock go down to a place with big computers and libraries and such.
Good idea. Not just for Spock, but the whole sciences department -- a section with lots of blue-shirted crewpeople working in labs and such.
How about a ready room for Kirk?
Maybe an office for McCoy?
McCoy was the only character who did have an office. It's the part of the sickbay set between the exam room and the lab. It's the second room from the left in this diagram:
http://www.st-spike.org/images/interiors/enterprise_sickbay.jpg
Do we actually see it in an episode, though?
Another thought I had: the obvious redressing (botanics = sickbay, conference room = pretty much everything, Kirk's quarters = Uhura's, etc.) actually makes things MORE realistic. I like to assume the (in-universe) designers of the E were more concerned with function than form and thus were constantly re-using the same basic room layouts to simplify construction and design.