A bit late to add to this forum, but I came in without an opinion and it seems fairly obvious after reading the comments that the Z-axis isn't well designed for this game.
Aside for the decorative nature of having objects at differing heights, the crippling effect it has on defenses and the use of the z-axis to defend carriers are signs that it is broken with regards to actual gameplay. Were it not for these issues, I would not mind its presence.
The problem with defenses is that, ultimately, they are designed to operate 2 dimensionally. You cannot place defenses on top of each other, over/under planets, and though you can cover a gravity well with mines 2D you cannot come close 3D. More importantly, if starbases have blind spots then the Vasari starbase becomes infinitely more effective - aside from AoE abilities - than any others. You can place starbases at different heights but this has no bearing on the fact that you can still get under or over them. In fact, against 2D players it simply creates a new problem. Even if you could rotate them this just moves the blind spot somewhere else - the starbase cannot rotate after it is built.
More importantly, arguing that the benefits of the Z-axis outweigh the loss is not really possible. Static defenses were the major addition of the entrenchment mini-expansion. Arguing that an almost-entirely ignored element of the game, the z-axis, should cripple this portion of the game is not reasonable. Neither is it fair to say that defenses are not used skillfully, for two reasons. First, including a game element not intended to be used with players makes no sense. If defenses shouldn't be built and are therefore overlooked in game design, why would they be included in game design? Second, defenses are sometimes a valuable way of guarding a valuable planet or chokepoint. Using turrets to supplement a fleet defense during a losing battle makes perfect sense, as they are cheap considering their firepower. more importantly, phase inhibitors force an opponent to seriously consider whether to attack at all, since any attempt to flee will require destroying the inhibitor or having a badly delayed withdrawal. Mines are similarly an effective way of slowing an opponent who is too powerful for your fleet to handle at present.
Sorry if you feel these points were already made, but several times after I saw them it seemed that the same arguments were used to support the z-axis. I'm not saying the z-axis shouldn't be in game, I'm saying that without a serious patch on its effects, it exploits design flaws in static defenses - besides the ability for carriers to ascend or descend unfairly far from the gravity well. If these problems were fixed (same vertical travel limit as horizontal and a vertical field of fire for defenses, for starters), I wouldn't oppose including the z-axis in gameplay.