As far as Java is concerned, I have tried straight JOGL/LWJGL, JPCT, LibGDX, and JME, and if you’re going 3d and want to actually get something done I really can’t see any reason to use anything but JME. I don’t want to seem like I’m bashing others efforts, but really JME really has the best documentation/support/features (ignoring straight opengl).
My only concern with that would be how detailed you want this city and its populace to be, which I guess would be the only reason to go for Unity or Unreal or w/e but then goodbye java.