They should have either kept TOS exactly the same, scene for scene or gone George Lucas insane, adding much more detail to the ships and alien crewmemembers in the background.
I think the latter could have been a lot of fun - I'd love to see Arex on the bridge manning a previously empty station, or Kirk and Spock walk past M'ress in a hallway. Replace the obvious pictures hung around the bridge with animated displays. Re-edit the Klingon fleet scene in "Errand of Mercy" so you see an enourmous fleet made up of a variety of Klingon ship types, one leading ship takes a warning potshot at the Enterprise. Have the M-5 take on an upgraded Phase II-style Connie, a Franz Joseph Dreadnought and a TOS-style Miranda. Add a window or two to the recreation room.