Love how C# is coming, reading the long changes thread gets me real hyped.
While the core content is more important, I've always wanted maybe some more details in law enforcement and justice within your empire, and more specifically, details into piracy and rebellion. Having a system where pirates can form, hijack shipping, form bases and maybe even re-invade your empire would be neat, like a weak (at first) empire that represents individual pirates and how their resources increase over time. Perhaps things like smuggling as well so you can have parts of your navy dedicated to interdiction.
Rebellions would also be nice, where they start at certain unrest and have stages (planning, covert, overt). Planning is where rebels gather resources and followers secretly, and then other phases like covert (where they sabotage and steal) and overt (where they outright fight the local governance and law enforcement / military). Perhaps it could be something like certain buildings and other things on planets get allocated to the rebels in the overt stage, and other special calculations otherwise (money and equipment stolen, rebel leaders, support).
Perhaps tying into this system could be maybe a bit of fluff things, like modelling of population centers on planets and their growth / names / impacts on other mechanics, and maybe small little details like statistics on minor civilian traffic at worlds (things like small shuttles, liners, recreational vessels and such that are too numerous and insignificant to be modeled by the game, but a statistic that could impact smuggling difficulty or tie into other things). Just some thoughts, and I want to get the idea off even if you don't want to go down that rabbit hole!