Orbital Placement
In the final game (or next beta) will we be able to place orbitial structures around planets along the z-axis? Instead of the yellow circle rings for placement there could be either a wire-mesh sphere or a faint transparent yellow fog that shows where around the planet orbitals can be placed. Similarly, the orbital footprints could be little wire-mesh spheres or transparent fog spheres that change colour as they do now for placement and such. Otbital weapons will have to be able to shoot in their sphere; with the obvious blind spots (like platforms in HW and HW2).
Movement
In the final game (or next beta) will we be able to move along the z-axis? It would be nice to move your fleet to a z-axis position, jump to a new system and exit at the same z-axis level. This has obvious tatical benefits when combined with z-axis orbital placement.
Resources
In the final game (or the next beta) will system resources be placed along the z-axis? This could free up space on z=0.
System Placement
In the final game (or next beta) will the systems be placed along the z-axis? Currently the game 'maps' are unusually flat for a space 4X. Using the z-axis allows for more creative maps. A somewhat similar game released last year (starts with 'Sw...') maps great use of the z-axis in its galaxy maps.
Currently z=0 gets crowded very quickly with all placement and movement occuring on it. It seems a slight step backwards in a game that appears to be taking quite a few steps forward. However, I like this game very much and look forward to testing the next release.
Thanks for reading,
Ride0
Thanks for the great comments 
Use tilde for Z axis movement. It works the same as HW2. You can remap the key if you like. Ships in phase space will arrive at the corresponding Z position of the destination. Building along the Z axis is a possibility that we aren't overly against, just haven't tested it fully yet.
However, we have experimented extensively with Z placement of the planetary and solar systems and the code still exists to make this happen but it just got too confusing. If there is enough feedback to warrant re-instating it we will give it another shot but for the moment it seems to add very little at a lot of cost.
We also spend a lot of time playing games that have tried this and also examined the player feedback on those games to get a feeling for how the majority of players felt about it. Again, the concensus was to keep the map relatively 2d.
Ofcourse, maybe someone here has a great idea how to keep the maps 3D without getting too confusing, I'd love to make it happen! 

It is difficult to identify objects in 3d. What I mean is that if you load up a savegame of an unknown battle-scene from someone else in Homeworld you will be confused for quite a while until you remember where what stuff is. Once you know which objects there are and where they should be it's easy.
So the basic problem is to move objects from virtual 3d space into your head. Not maintaining them once they arrived. HW shows that, if you can keep track of all game-world objects, it's fun and intuitive.
So true 3d space is useful when the absolute number of objects is limited in such a way that you can look at a system and remember that there should be a starbase somewhere 'above' a specific planet. If you don't remember that it'll take ages until you find it.
So in a system with 4 planets and a couple of asteroids this is possible. But in bigger systems it'll be confusing.
But generally I don't like the thought because all real systems are aligned in one plane. Right now all objects that should orbit in a different plane are currently located, by accident, in the natural plane. I'd only support true 3d systems if objects in SoaSE orbited properly.
I dont think placing planets etc along the Z axis will be a good idea at all. It will simply confuse. It works out in a game like "Sword of the stars", but that is also turn based, and in a rts game like this, even a slow one like this i think it will bring nothing but confusion.
If you havent played a 3D strat game like sword of the stars it all might look good on paper with 3D map of planets. But in reality its not, and even less so in an RTS.
A second reason for it working in SotS is that you arent bound by phase lanes like you are in sins. This exact game mechinism makes any talk of a 3D map purly cosmetic, since it will add exactly zero gameplay change. Also in sots you can intercept fleets in midspace, which is another reason for a 3D map. In sins it will simply be add confusion.
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