Timo, just to clarify for the TOS version - how are you handling the hallways and foyer that lead into the shuttle area? I've approached this problem in 3D and there are only a couple of good ways to do it. But if you're not using them, then you've got more options. Just curious
Pardon my quick'n'dirty brutalizing of Probert's familiar sketch:
Basically, this is how I see all the three ships being essentially the same. Each has this big cargo cavity in the middle of the secondary hull, although only the TOS ship has it extending down to the circular ventral hatch. Each has three elevators, but only in the TMP version are they exposed, thanks to advances in forcefield tech. In the others, they inhabit a separate compartment where shuttlecraft are kept at readiness, behind a pair of rolling doors (with a turbolift between them in ST5:TFF, and a turbolift or corridor or perhaps both between them in TOS).
Only the TMP version also strips off the inner side walls of the flight deck, eliminating the corridors beyond (and substituting workbee hives). The other two have the transverse observation deck, with windows both into the flight deck and into the paired hangar-elevators.
Oh, and the TMP and ST5:TFF ships have vertical warp cores, a bit farther aft than Probert postulated, while the TOS ship has some other sort of setup above the cargo area plus horizontal leads to the stems of the pylons.