I would say the two biggest differences are in the diplomacy/event system and the way the various factions are differentiated from one another.
Many things you do in the game create "Issues" with the other factions, which not only affect their attitudes towards you but can also be actionable items that you can interact with the faction over, to either resolve the issue (or inflame it, if that is your desire). For example, if you colonize a planet that a faction had planned for colonization themselves, this creates an Issue which is then visible in the diplomacy screen; you can view it to see the effect (a reputation hit), and you can click on it to start a conversation with the faction leader about the issue, to possibly eliminate the penalty by offering compensation, etc. We are trying to add enough faction-specific dialogue options to make these interactions feel engaging and to immerse you in the world of the galaxy, and we have events firing off in the background to insure that there are always incidents which will create issues even if you are not actively creating them yourself.
Each faction has a set of custom ship hulls (with different component slots) and some unique technologies, some of which can alter gameplay in significant ways. The Gremak, for example, have access to Marauders which allow them to raid colonies for slaves (rather than simply invade or destroy the colony), and the ability to trade slaves and use them in their local economies opens up new gameplay options.