I hope you are joking here. Surely it is obvious that all that is required is a small tweak to the co-ordinates of the system locations. That's hardly "can't be fixed".
The galaxy in this game is... how to say it, an involved beast. There's no place that really stores all the systems or even their names, stars, planets, etc., only additional information like who discovered what. Most information is generated on the fly, and it depends on what's going on around it. So if you move, add, or remove a system, "everything" changes (at least in a huge radius). So changing that "chunked" approach to distributing stars would mean no more Colonia, no more Beagle Point, no more Pleiades, no more Bubble as we know it today. And considering how much time people have spent on discovering and developing all that, keeping a bit of a boxy appearance in some areas seems like the better move.