I think a true 3D roguelike would be fine if done right (which is difficult, especially the presentation). My vision is a game where e.g. archers and mages could defend their cities by standing on the roofs of buildings and shooting, summoning floods etc. And the mages below could cast "pull" spells which would pull them forward, causing them to fall from the roof and hurt themselves.
And, the roguelike idea of display is that it should present information in a way which is easy to read. 3D display of a 2D game does not have this property. But that's not a big problem, of course. And it encourages all those people who cannot play a game unless it is 3D.