Its mostly based on what people have with them at the moment but there are certain advantages of 2d and 3d terrain.
Grid terrain e.g. Descent/D&D starter terraine has some closed spaces and forms a maze, so it is hard to charge , integlible characters have more use and ranged attacks are less effective. New empire formation Yuri , Macbeth , Liliana & CO would abuss this kind of terrain and nearly all wissenshaft units would get their asses handed to them in such a board.
As for 3d is some kind of standard for anim tactics game, as you can see the rulebook uses non grid board as a default. But even 3d has its flaws as you come up with multiple elevations and really high towers. This makes AD characters powerful as hell because not only they can start in such position but climbing ther usualy would mean spending 2 extra move actions and sometimes your character would be unable to put his mini on the top beacuse the enemy mini uses too much or all the space there is. You can imagine how Cordelia, Goethia and Daniel abuse elevations.