Sorry guys. The game was made with these limits purposely to keep the game feeling more like Trek and to make the game playable by as many people as possible.
Star Trek has a history of film space in a very tall starships sort of way. It was decided that to allow full 3d space flight would remove that feeling from the game and make it feel less Trek-like.
Also, though many people can deal with a fully 3D environment there are many others that would not and would find the game too difficult or annoying to continue playing. The current style reaches the largest demographic possible and alienates no one. This is important when you're making a game you want more than 100 people to play.
Sorry, but the limits to the Y and X axis are here to stay. I'm not sure the game engine would even be capable of such a change.
There is another issue in this as well. Turn rates would work in all three dimensions. Escorts already have a huge advantage in the turn rate field, you would only multiply the issue if it was available in a third axis. Add to that some ppl's inability to function in more than 2 axis, and, well.. you would drive a lot of ppl off.
Don't get me wrong, I would LOVE three dimensional combat, but I also understand why it's not there. (and shouldn't be)
Thoose arguing that "it feels more trek" when not being able to loop, should think back to such episodes as ENT: The Expanse, where Archer loops above a klingon BoP to get behind it, or DS9:Fortune Favors The Bold (either that one or the next), where the Defiant loops around a Bug ship, to take it down from behind.
It would also remove the anoying PvP thing where everyone ASAP rushes to the top of the map to have a better position.