The Enterprise-D is freaking massive. There's no way we were ever going to see whole parts of the ship largely due to budget. Unlike TOS, we got an actual shuttlebay set to represent the twin Shuttlbays 2 and 3 on the back of the neck, technically part of the Battle Section. The main shuttlebay was much closer to the bridge, just a few decks down, and massive. I believe it was only see twice. The first time was "The Best of Both Worlds, Part II" from Data and Worf's perspective inside the shuttlecraft. We see the bay outside the window as the shuttle launches and zooms past the battle section. I always loved that shuttle sequence. The second time was the exterior when the main shuttlebay door rolls open to decompress the bay and push the Enterprise out of crashing into the Bozeman. Why not build a miniature set? It would have been awesome to show shuttles coming and going.
Next up, the Captain's Yacht: it would have been nice to see this in action at least once. While separated, they could have cheated and just used shots of the ship that don't show the underside of the saucer.
I'm guessing never saw it, because a story just never came up that justified using it. In reality, if Picard did fly off in his yacht, it would likely be some safe, boring, diplomatic mission that might not exactly be entertaining for the audience. 
Saucer separation: we got to see it 3 times on the show, once more in Generations. Voyager did their landing gimmick once or twice a year. Given TNG had 26 episodes per season (except S2), maybe they could have gone the same route: use it as a special annual gimmick or something?
Another thing I'd have liked to see, rooms like crew quarters, but with the windows facing down instead of up. I know, I know, budget.

Next up, the Captain's Yacht: it would have been nice to see this in action at least once. While separated, they could have cheated and just used shots of the ship that don't show the underside of the saucer.


Saucer separation: we got to see it 3 times on the show, once more in Generations. Voyager did their landing gimmick once or twice a year. Given TNG had 26 episodes per season (except S2), maybe they could have gone the same route: use it as a special annual gimmick or something?
Another thing I'd have liked to see, rooms like crew quarters, but with the windows facing down instead of up. I know, I know, budget.