And now that I have a couple more minutes, let me also try to be constructive.
The "2D/3D universe" question is actually two questions:
1. Does the universe have a flat 2D structure, or a volumetric 3D structure?
2. If the universe is 3D, how can that information be presented to players in a way that's easy to manage?
It sounds like there will be some 3D-ness to the structure of the universe (at least in part). So this really comes down to how to let players see that structure in a way that most of them will be able to easily understand and manipulate.
Gazz offered some suggestions, but I wonder whether most of them actually trade one kind of complexity for another. Using additional abstract information (e.g., ring size) to stand in for height is not necessarily easier to understand than showing the actual 3D relationship of star systems to each other.
A frequent objection to presenting 3D system connections as an EVE-like web of points is that it's hard for some people to work with that structure. The combination of scaling the web (zooming in and out) and rotating it around the current zoom point, is described as a real problem for some gamers.
I'm not about to argue that it isn't. But instead of using that to argue that the universe shouldn't be 3D at all, why not focus on improving the presentation by simplifying the web model?
One improvement might be to limit the number of star systems displayed at a time. Josh has showed us a simple generation of a group of something like 20-25 star systems. Why not make that the standard? Say that groups of 10-20 (on average) star systems constitute a "sector", possibly with some characterstic in common so that sectors are easily distinguished from each other in the memory of players. This way players are only dealing with a manageably small number of star systems at a time.
(Note: With my gamer hat on, this isn't the approach I like best. Like I've said before, I much prefer a continuous universe to one broken up into discrete points. But I can compromise. In fact, I think it would be OK for this universe map to be "flat," given that it's a closer analog to the galactic plane than individual star systems.)
The "universe as a collection of connected small sectors" model suggests a second improvement over the EVE-style map, which is to not implement scaling at all. When you're trying to grok the connections among hundreds of points, it's nearly mandatory to be able to zoom in and out to see smaller parts of the web at one time. If you limit the number of points to no more than 25 or so, however, they can all be displayed at one time (with some judicious map dragging) with no zooming necessary. That simplification of controls would, I think, go a fair way toward making this kind of map more usable by people who've found other 3D maps cumbersome.
So I suggest:
1. Define the universe as a flat web of connected star sectors.
2. Define each star sector as a 3D web of 1-25 connected star systems (with 10-20 being the average).
3. Let 1-4 of the star systems in a sector have outbound links to other sectors.
4. Display the universe map as a plane of sectors, allowing zoom-in/zoom-out to areas of the map to show about 10 sectors.
5. In the universe map: left-clicking a sector brings up the sector map showing the star systems in that sector; right-clicking a sector displays information about that sector (number of star systems, total population, primary political "owner" of star systems, etc.).
6. Display the sector map as a 3D network of star systems, allowing click-and-drag to rotate the web around the (predefined) center point of that sector.
7. In the sector map: left-clicking a star system sets it as the destination for the player's currently designated ship/fleet; right-clicking a star system displays information about that system (star type, number and types of planets, system ownership status, "specials," etc.).
8. Both the universe map and each sector map will have "information" modes that allow players to a) filter for particular characteristics (location of player ships/fleets, high-population worlds, metal-rich worlds, cargo destinations, mission targets, uninhabited worlds, unknown/unexplored worlds, etc.) and b) visually highlight sectors/systems meeting filter criteria.
I've been on the wrong side of several LT design plans already, so I won't be surprised (or offended) if this suggestion is also rejected.
But I did at least want to put it out there for consideration, if for no other reason than to maybe help spark some additional thinking about how the structure of the LT universe will affect not just mechanical but dynamic and aesthetic aspects of the game. All those modes of play matter -- not in the same degree to every individual player, but in some degree to all players.
Nobody said building a universe would be easy.