I think the main problem is that it really doesn't add as much tactical depth as some people claim it does so it really isn't worth the added complexity.
Ok, I like 3D movements, but I won't lie to myself that the reason I like that system is because some tactical depth reason. You're absolutely right, there isn't much things to add in term of tactical. To be honest, Hegemonia has that system, it's so useless that most of the time I forgot it was there,
Nexus: Jupiter incident (notice the italic) did it so well by itself that I don't need to do it by myself, Homeworld? Yes it's there, but only on the hardest level of PDF mod that I need to use 3D tactical movement, most of the time, again, I forgot it's even there.
The battle system in Sins is pretty simplistic. I don't mean to undermine the game btw, I'm perfectly fine with it understanding this is a 4X empire bulding&space combat hybrid game and not a hardcore space tac game. What I mean is it's safe to say the game will need a hell load more features for the battlesystem to actually justify the need of a 3D movement
tactical depth wise (Shield orientation, fire angle, point defense, blank point, turning rate, hardpoint ...etc...). So yes, let me repeat, you're correct when you talk about tactical depth since honestly, 3D movement will add little to nothing in that department IMO.
Now let's talk about the oversight that I think you're making. Tactical depth isn't the only thing that a 3D movement add however, there is also presentation, and 3D movement add A LOT to that area.
Like I said, although most space game have 3D movements, they're done automatically, while the players mostly pay little thought, this makes the battle look real. It's space, you have ships on the top, on the side and under you. Also, having 1 extra dimension allow more possibility to make shift during engagement (think about it, having another movement vector means you have another 360 arch of movement). Maybe I haven't play all of them (although I dare say I play a lot) that Sins is probably the very first game and only game I ever saw where spaceships come to a complete stop when they engage. In all other games, the ship still make a little shift in the movement even when they lock into a target. Realistic, coolness, exciting ...etc... you name it.
Ships moving isn't much a problem if not combining to the 2D moving of most ship. Becuase like I said, for the presentation it doesn't feel like Space. Right now it feels like we have a bunch of vehicle running on an invisible ground rather than flying through space.
(up or down, you still can't get any further away from the planet than you would on a 2d plane since it's a spherical arena)
It is, when you have a lot of stuffs and something is trying to run through. If you consider the evelation is like a lane, while relating to a planet their position is the same, but having 3 structure on one evelation is like having 3 obstacle on 1 lane, and you only have one lane any way. Having 3 structure on 3 different evalation, even if you only use 1 lane, it stills mean there is only one obstacle, and of course, if you use all the evalations, it means you have 3 lanes (relative number figure ofcourse).
Which leads to another problem, traffic. I haven't test the lastest built yet so I don't know if this was fixed or not, but usually it kinda funny seeing the automatic ships (trade/refinery ship) have to zig zac around my facilities to get to their destination and lot of times ... get stuck (I once had a trade ship got stuck at a refinery for about 10 minutes before he could get away). Again, presentation wise, it feels like a truck running on an invisble ground of a crowed street while it has all the space above and below for itself.