You know, like the ones from Star Trek Insurrection or DS9's episode "The Siege"?
First off, not all starships have the ability to enter a planet's atmosphere, so such missions would give players a reasonable excuse to change ship to a shuttle or a fighter.
Second, these could be both combat and/or scan/puzzle oriented, depending on preferences. As much as I enjoyed fighting in a shuttle, neither The Vault nor Operation Gamma gave me much opportunity to do so. Funny when you think how many "destroy X waves of enemies" types of missions there are in the game for starships...
Third, new areas and surroundings would be a great change for STO, and I don't really think they would require THAT much work. They would basically be big "space" maps with a ground texture at the bottom, while the rest could just be invisible walls, as in any other map. Depending on a mission, there wouldn't be a need to create complex ground environments (mountains, trees, buildings), at least at the beginning, as most of the action would happen in the sky, with the landscape being only a cosmetic.
Fourth, some new mechanics could be added to spicen up the gameplay, like clouds or ion storms (depending on the planet) having various status (and visual) effects when entered (similar to the nebula static effect in The Vault). Would be especially great for shuttle PvP. Also, if you're worried about players reaching the ground, just add an explosion/insta-death effect there (again, I don't believe this should be difficult, especially for a flat surface).
Fifth, just imagine all the ideas for the missions you could do! Not sure how many of you played the Ace Combat series, but those games had really great and varied mission types. Dogfights, military installation bombardment or defense, fightinig an enormous spacecraft that has entered the atmosphere, and many more.
Just a thought, but in all honesty, this is my number one thing I would like to see done for shuttles in STO. Not shuttle pvp or some other racing thingy.
Shuttle Racing Type 1
To some maps you could simply add Navigation points first one to hit all Nav points (In Order) wins the match
Again Daily/Event listing for repeatable goodies Dilithium/Level appropriate Item etc.
A good example of an existing map would be the One with the swarms and asteroids from the New FE put Nav Points at the entrance and Exit of several asteroids (This keeps a semblance of a track as you can't just skip out big bits of the map) Have all weapons/abilites turned off a straight race, best pilot wins.
Each Factions respective fighter shuttle are the only ship that would win, as they are both the fastest and most maneuverable ships in the game.