I dono if anyone has suggested this yet... But what about wormholes? Like natural wormholes that dont lead to the neighbouring system, i mean unstable wormholes which can lead to anywhere in the galaxy! Would make things interesting if you found one and succefully got a scout through to the other side of the galaxy, maybe even a colony ship? It would be tough though, and you could very easily lose many ships trying to enter it. This could tie into moral to, if you send a colony ship with millions of pop to their doom and then try to send another one (especially right away) the ships (and systems/empires to a lesser degree) moral would take a hit, but naturally they would follow your orders anyway (being the supreme ruler and all). But what if that ship is lost as well and you try AGAIN? The moral of the next ship would be even lower, eventually you could get to the point where the ship refuses to follow that particuar order, knowing it means their doom, and quoting some human (or Abbion/whatever) rights act you thought you got rid of
This could spread empirewide, happyness would fall and there would be a public outcry for your actions.
Would be interesting, these wormholes could lead to new and fascinating destinations, and be very strategically valuable but could also be a very bad thing if your not careful.