Please keep your "brutal honesty" to yourself. I insist on at least an attempt at civility from my children, let alone from supposedly intelligent adults. People on the internet seem to think that "honesty" and "courtesy" are mutually exclusive. Other people on the internet seem to think that "courtesy" is conversational weakness. Neither is true. If some sort of mutual courtesy is impossible between us, then it is impossible for us to converse.
On to some points....
So, let's see if I can envision and describe my vision. I am at a planet/star zooming about and decide I need to go to another planet. In present visualization, I click on my ship and and click on my destination. This is straightforward. It does flatten a galaxy, which is a bit much since galaxies are actually very thick, but then again thicknees to width ratio makes galaxies thinner than paper, if I understand correctly. A lot depends on what level of visualization you can muster. This flattened galaxy perception seems to be fairly universal to anyone I have watched while they looked a galactic map. It made sense to them instantly.
Now I am looking at a 3D representation of space. Not a galaxy disk, but a 3D chunk of one. How do I arrange the same general overview with planet A and star B so that I can see them at the same time? My experience so far is that the orientation of the camera in 3D is a constant adjustment. You mocked me for bringing up Assassin's Creed, but judging on my experience with that game, orientation in 3 space, especially with some sort of follow camera, seems a non trivial exercise. For programmers and users both. It's not just my lack of eye-hand coordination, it is the constant need to turn around and around to get an overall view of things. It strikes me that it would be a distraction from the strategy level of the game to deal with the visualization. Maybe it something I could learn over time. Maybe not. Do you have words of encouragement on that point?
Am I looking at a 3D array of cubes? Am I looking at things in 3D polar coordinates? If I want to single click to my destination, how does the PC know what I mean in terms of depth perception? I still only have 2 dimensional screen and mouse pad to work with. I have dealt with interactive three dimensional displays in various experimentation levels. They all needed some sort of actual 3D input device to make intuitive sense. I do not see how to get around that in a clean UI manner. If you do, and can get it across to me, I would appreciate that.
Note, I am expecting that we are not doing the 3D equivalent of a first person shooter and everything is done from the viewpoint of a single space ship, that we are dealing with some sort of over all view. Also, I am not talking about space lanes, but actual 3 space. Both are valid views for other games, but not what I am hearing you say as a fully 3D 4X game. If you see it different, please let me know.
What do I gain in game play moving three dimensionally? Some gamer friends put together an interesting real life version of space in 3D. They took the list of the nearest stars, converted the polar coordinates in the reference book to x/y/z, took an empty bedroom where a room-mate had just moved out and hung little balls of glow-painted styrofoam according to the x/y/z coordinates. They had a 3D simulation of near space. It was a great effect. For a while. You could move around and see the various parallax effects. Then it got kind of meh. You stood still and your eyes saw a 2 dimensional display of bright dots without depth. As we stood in the dark among the stars, we talked about 3D as gamers. We couldn't see where it would add to movement, to maze and obstacle avoidance, or battle. Especially battle. It was either dogfights in space, or big blobs of fleets going at each other. The dogfights bring out the tacticians in everyone, but they quickly came to the conclusion that battle without terrain is much less interesting and variable. In fact, it seemed that a lot of the things that made that made strategy enjoyable in many ways got lost in the addition of another dimension. It was just to easy to go around anything. All battles were effectively without terrain, all goals just a minor detour away. On beyond the visualization, what will make being in 3D strategically interesting?
Not as coherently stated as I wished but an offering of polite conversation as best as I could conjure.