Creating missions to use all 3 dimensions is easy, making the player aware that action is actually taking place in 3 dimensions, that's trickier.
As mentioned earlier, players tend to redefine The Plane as the mission goes on, depending on were The Action is at any given time. So if you want to give the mission a 3D feel, you need to invest some time and effort. Here is an example approach :
- Define a standard plane or vector for the mission
(eg. capships in parade formation, a space station, ship going from A to B, etc.), and make the player aware of that plane
(show a bird's eye view of it, either through a cutscene or by having the player fly towards the plane-defining thingy, etc.), then you can play with the direction of the Action to highlight it.
- Make sure the player regularly intersects with the plane or vector, or at least have it in view when having a new point of interest pop up.
- You can also use the starfield to help construct points of reference, for instance : have a planet on the right, a moon on the left, a pair of suns behind, dark blue nebulae in front, bright yellow nebulae on top and an empty starfield bellow. Or any number of big background objects, really (see the Karos graveyard from the Homeworld series).
And of course, you always need to keep this in mind :
The issue is that to make a space actually playable, you generally don't want a massive number of entities moving fully in 3D space. Keeping track of all that is a nightmare for a player and will get them confused.
And it's a lot of added complexity for the mission designer.
tldr;
Making 2D missions : trivial
Making 3D missions: easy
Making the player aware that he's in 3D missions : tricky