The setting is the biggest problem. You can choose realism or not. If you choose realism, you must choose a solar system or an interstellar setting. If you choose a solar system, there are problems of the movement of the planets and of acceleration of bodies that cannot be represented with regular civ movement. If you choose interstellar, you get light speed as a limit that deals with unit acceleration, but you no longer have the plane of the ecliptic making things two dimensional. You can do scale telescoping and have the star systems be big islands. Most of your land will be Oort cloud, maybe one ring of Kuiper belt and a core square of "planetary system."
Any interstellar civilization will have something more advanced than solar power. If not fusion (which is not so much a tech as just having the will to go large enough in scale), it will have mastered charge parity violation well enough to produce antimatter-matter pairs in ratios skewed to antimatter--essentially meaning free limitless energy and conversion of any kind of matter into any other. Thus there will be no concern over resources and no variety of terrain, which is kind of dull.
Then there is the option of focusing on a single planetoid system. Let the whole map be the asteriod belt, kuiper belt, or oort cloud with only a small part in the center occupied by the inner planets (not individually represented, except as jump crazy resources). This not only makes the game easier, but it is a realistic representation of relative scale and the plane of the ecliptic which is conveniently two dimensional. You can still use the speed of light as a speed limit if you change the time scales per turn and say you can only go up to a certain percentage of light speed per tech advance due to relativistic limitations.
(The rings of saturn are also a good setting, but like all single planets in a larger space civilization context, there is the question of why the research spending of one civ of this planet is so significant. )
One cool way would be to have the map represent different things in different ages.
At first, the inner map could be the planetary system and the outer map the asteroid belt. Age two: the inner map is the planetary system and the outer map is the kuiper belt. Age three, the inner map is the plantary system and the outer map is the oort cloud. How? Call the outer map terrain "planetoid belt" and have new "resources" (that look like asteroids or ice worlds or comets) appear, concurrent with the new age. Of course, that leaves the problem of non natural aspects of geography. When I went to the Kuiper Belt age by discovering Fusion Rockets, why is my city that was in the asteriod belt now in the Kuiper belt, if this map is supposed to represent something new? Maybe this could be glossed a little with abstract names like City One, but there's not much getting around it.)
Roads should be just lots of tiny dots, representing lanes of many space vehicles travelling jetsons style. Shield producing improvements should be factories rather than mines, and irrigation should be space habitats. Food will not be a problem to synthesize, living space (and attendant life support developments) will take its place functionally as what allows population to subsist and grow. Forest should be an even better kind of space habitat, space megahab, that you can produce with a higher tech. And you could start with everything "polluted" , ie undeveloped, and "develop" it ie clear the pollution. Most of the terrain could be marsh (raw planetoids), which you can eventually clear to grassland (nanoconverted planetoids). (Though those will of course look different on the screen). In nanoconverted space you can make megahabs, which can be built in conjuntion with space factories or more habitation. You can not only build space lanes but teleportation terminals (use daftpanzers roads from space wars perhaps). Finally, you can harness vacuum energy itself to create great gobs of matter from nothing, with the right buildings, which shows up as pollution at first, but eventually converts the forest into Mountain, with global warming effects, which is Dysonsphere perhaps, many AU wide spheres with new planetary systems inside them. The planetary system could be Hill, which is prime, but limited.
And in between you've got all these other techs you could make a part of it.
Just some ideas, maybe some will help this come to fruition so I can play it sometime soon seeing as how my solar system mod didn't work out.