I seem to recall something said about much of the ship being available for expansion at later dates, back at the beginning. And of course the Whitefire plans show the original idea of a vast communal "mall" area in the saucer. (Not a shopping mall, just a big social area).
One idea I actually like from NuTrek was the vault. It would help rationalize all that space if the Enterprise was carrying a ton of artifacts and specimens from various exploratory adventures on a long mission outside Federation space. Unfortunately after the Borg threat appeared, we didn't see the ship venture very far from home or for very long.