I think it would be a nifty little addition to STO to have ships with moving shuttle bay doors. We've seen them in the series quite a few times, and it would be cool to see them opening and closing when we use Boarding Parties, Consumable Fighters, or in the future, worker bees or that "Default Small Craft" button some devs have talked about.

Along similar lines, I also think that the "Captains Yacht" should detach from the underside of the Saucer if you are in a Sovereign or Regent, like we saw in Insurrection.

Well since we never get to go to our own shuttlebays, working doors seems a bit far off.
Working doors would require the art department to create animations for the dozens of different doors that these ships have and creation of a hanger space that would be visible beyond those doors (although they could probably get by with a glowing atmosphere containment field that would hide the absence of a hanger beyond)
My ideal view for this would be after you go to your hanger and select a shuttle, you are treated to a cutscene of that shuttle leaving the bay before you are returned to the shuttles bridge view, likewise when landing in the bay you get a cutscene animation of the process ending with you standing outside of the shuttle in the bay.
I wouldn't mind a similar sequence for when you hit the docking thrusters when close to Earth Space Dock allowing you to experience the process of mooring your ship.

This all would probably be regarded as useless coding by the developers since it adds nothing to actual game play and may actually become a distraction if you are in combat and have more important things to do than watching you bay doors opening and closing.

Well if we are talking about things far off then I would like a mission where we have to properly land our shuttle in the shuttle bay from space. (That way I can practice "Emergency Landing Plan "B"" )

I would also settle for landing the shuttle on Vulcan during diplomatic orders.

I like it. We could also use a shuttle race. That would be fun!

Besides, most ships don't have large shuttle bays, and you could create one shuttle bay, and just scale it according to the size of the ship. Not all ships would need one anyway, as on a few ships we don't even know where the hangars are. But it would be a nice touch on ships like the Excelsior, Galaxy, Connie, Intrepid, and the like. You could even have the Atrox raise and lower it's hangar containment fields when fighters are launched!