Consider, for instance, the ships. As is the case in many games, Pax allowed you to design ships based on available technologies, and those technologies would improve over time. Unlike other games, however, the user could actually design the technologies. For instance, one might design a gun that does most of its damage only at long distance, and none at all at short range. This would allow you to make ships that would keep their distance and "plink" at their targets. Or you might make a weapon with the same power but with short range, which would be cheaper to build. Then you would try to close with your targets and bludgeon them.
Or consider planets. In Pax, the solar systems moved in realtime, and included not only planets, but moons. Moreover, the planets, depending on their size, had multiple "territories". If you took over one territory, once the population grew they would naturally try to move into the surrounding territories. If these were inhabited by an opposing player, fighting would ensue.
Additionally, Pax's galaxies were "open" in the sense that one could fly anywhere. This contrasts with most games where ships in flight are basically nowhere. This had advantages; you could place ships with little other than sensors in deep space and use them as an early warning system. Or place one in an opposing solar system and use it to spy.