I have a mild preference for flat terrain over 3D for a number of reasons;
1) easier to transport and store
I do most of my gaming at a local gaming club, so any terrain I want has to transported meaning MORE boxes/bags to lug to and fro, and store in my rather small house. Flat printouts fit in a folder, not taking up space better used by fleets (and are lighter

)
2) Construction time and cost
With flat terrain, all I have to do is print and cut out, making it easy to resize and tailor, rather than hunting down the right size of materials, chop them up just right, base them, texture them (as appropriate) and paint them, using time and material better spent on my backlog of lead (ok, pewter)
3) more resistant to damage
It's hard to knock over a sheet of card on a table, and even if you do manage it, bits don't break off. The only real threat is spilled drinks (which shouldn't be in the middle of the battle field anyway), plus they don't risk transport damage
4) Easier to measure/move through/around >>> Faster gaming
With 3d terrain ot becomes harder to run a ruler at model height to determine ranges if it passes near/ through terrain, and as for moving a ship into or along the edge of an asbelt(the stem isn't in there, but half the hull of the model is).....aargh!. "Hold on while I shift these representative asteroids out of the way (trying not to damage them (or my ship) in the process)". Also without a template the location of the edge of the field can become more debatable (from the stems? the edges of the asteroid models?)
I will concede that 3d looks better,and can produce prettier pictures, but that just isn't enough of an advantage for me.
After all, your ships are 3-D are they not?
Well, yes, but so is space, and it's being modeled by a 2D surface, so logically, the scenery (as part of the 2d space) would be 2d as well :wink:
Anyway, the ships are the stars of the show/game, so they should look better than the extras/scenery
