Can't you offer options at game generation?
Like one that flattens and distorts completely, one that flatts by 80% and then clusters the result, etc?
Given that you're already experimenting with it, the cost must be there.
Though I certainly think full 3D would distract me from the game.
Reducing all heights by 80% and clustering would be my favourite, that way, one could still watch it from "above" for simplicity, only the jump distances wouldn't be properly represented.
Which I wouldn't care for in the first place, it should be possible to select a task force, then select a system on the map, and it tells you how long a jump would last at, say, 1000kms.
Or daily acceleration, or whatever.
What do I care if the jump duration matches the shown distance, if I can actually see both if I have to?