Hey, am i the only one that noticed that space is 3D. Although I have yet to play it (its shipping now) I have noticed that the game plays out in 2D. If im wrong, sorry, but Im pretty sure about this.
Planets, gravity wells, and star systems tend to be on different locations of the z-axis. Also, depending on obstructions ships will sometimes go up or down on the z-axis all by themselves and not everything you place in orbit is on the same plane in the z-axis. It tries to give the illusion of 3D without the complications of 3D. There are unused key-bindings you can set to give yourself 3D control over your ships, but for the average Joe out there the full 3d environment and positioning can over-complicate things. It seems that Ironclad/Stardock wanted to keep positioning easy for fans of other genres and other games to get used to, but still maintain the appearance of a 3D environment.
Using 3D positioning is very easy for some people to grasp, especially if you've had modeling experience. However, not everyone can handle it so that's why it's an option. There are complex issues of control preference when dealing with a 3D space. For instance should the planet well grid:
1) stay flat and allow you to set an xy location and then drag or mousewheel to set a z position? or
2) adjust to maintain a circle according to the player's viewpoint so that the camera or gravity well grid must be manipulated instead of the individual positioning? or
3) use multiple gravity well planes so that you can set your ship onto one or another hopefully without accidentally selecting the wrong plane or wrong location?
Some people will like it one way, the other, and the plain 2D system. Personally, I feel that 3D would over-complicate battles in the RTS environment. Better form would be to allow full 3D control, but better function would be to restrict things to 2D. The developers had to balance this form vs. function dilemma and I think they've got a solution that satisfies everyone since the support for 3D movement is there but not automatically turned on. I think full 3D would be overwhelming at first especially to new players (they're having a hard enough time with pirates and AI initially).
This is just my opinion though.