The planetary movement thing is pretty incredible. I wasn't sold on it at first, but it is fun having to go through all my planets and reorganize things when a planet or two get's disconnected from my main cluster.
A really cool addition to that feature would be external stellar objects.
A rogue planet would come from outside the current system and have some kind of unique characteristic to it, such as increasing economy, research speed, upgrade all weapons/hull/shields/anti, have phase lanes to all planets, etc.. It could make a straight line through the star system and, obviously, only be available for a limited time.
A black hole would either pop up inside the star system or, similar to a rogue planet, intersect with it. The blackhole would alter the orbit of effected planets so that some get thrown out completely, get sucked into the black hole, change orbital direction, or change the plane of orbit (3D orbital mechanics!), etc.
White Dwarfs and Neutron stars could, again, come form outside the star system and create temporary or permanent new star systems. For example, a dwarf or neutron could come into the star system and pull five planets to them creating a new star system like in sins 1.
I am really liking the planetary mechanics thing and hope you add A LOT more to this. I'd pay down the line for an advanced mechanics pack for sure.