Haven't played the game, but maximizing surface area for cooling would work. IRL, cooling is a big issue for space craft that do more than just coasting with an occasional short course correction burn. Space might be cold but its near-vaccum is an incredibly good insulator.

So if heat management is a thing in a space game, this would encourage ships with more surface area (so non-boxy, non-circles). At the same time logistics within the ship would favour boxy/circle-shaped ships, so you'd have two contradictory design goals requireing you to find a good compromise between both. That should lead to some more interesting designs.