That is a terrible problen, what happens in your case, with increasingly narrow axes is (likely) unavoidable when you get very different span in the different axis-directions - a 2-by-2-by-2 brick-wall will be reasonably cubic and we can have a nice plot, if we extend this in one direction (2000-by-2-by-2) and display it with equal scale in all direction the largest span will force the others to become very small onscreen.
No solution, only advice: use judgement and "design taste" to the best of your capability for this problem.
HTH