A few suggestions for Sins2:
Phase lines make no sense. In space, you can fly in direct lines from point to point except to avoid storms or planets or stars or other phenomena. But, generally speaking, flying from planet to planet within a solar system makes sense. Phase lines don't, really. I realize they add a strategic component to the game but I don't think it fits within the fictional universe very well. A universe that makes no sense isn't fun. I do basically agree with a single phase line between star systems, that seems to make more sense than between planets.
Regarding planetary systems in the game, they're all based on a flat 2d plane. That's not realistic either. They should all be 3d around their parent star, with some of the planets with different orbits, speeds, and even some outside the primary elliptical plane. Furthermore, the planets should rotate around their star, like any planet does. Flying time from planet A to B would not necessarily be the same from one time to the next due to constantly varying distances.
More variant star types, including where the color of the star also determines the relative star size (red being very large, blue being very small) double stars, moons, nebulas, black holes, and other universal phenomena would all be nice additions too!