Even different flashpoints... In Black Talon was the Captain killed or let live? Was the General killed, or did you let him live? Which choices are canon? Neither of them, at least until for some reason they need to make a choice because for some reason they are not continuing our story but making an entirely new one.
According to Wookieepedia on all the class characters, all republic characters are lightsided and all Sith Empire characters are darksided. I take this to mean that the flashpoints would also represent that.