I don't if there its any hope of getting any of this into SE5, but here it goes:
Trade:
1- Valuable luxuries, unique resorces and bonus resources. A knock-off from Civ3, but it would make colonization more interesting. These resorces should be scarce, which would of course make the planets containing them very valuable and a source of conflict.
2- Trade routes to block and attack. Maybe a continuos line through several warp points and systems.
3- System blockade. The ability to blockade a system by taking the warp points on the opposite side, so not trade can go through.
4- Trading of luxuries and unique resources like in Civ3.
5- Copying another game its not bad since everybody does it!
Colonization:
1- Colony dome, a colony dome should be built first, and its size should determine the number of facilities and population size that it can hold. This dome should be upgradeable to bigger sizes.
2- Reusable colony ship. Only the colony component should be "destroyed" to build the new colony, not the whole ship.
3- Spaceports per every planet.
4- Starlines to connect planets and systems, not under direct player control.
5- Colonization of planets inhabited by other races, low tech or primitive races.
Trading Posts:
1- Trading Posts in planets inhabited by primitives.
2- Trading Posts shouldn't need population.
3- Trading Posts should allow the trade of luxeries or unique resources produced by primitives.
4-Trading Posts should be far cheaper than colonies, and could be fortified.
Colonial politics:
1- Relations with primitives
2- Colonial goverment, from military goverment to autonomy within the Empire.
3- Colonial militias for planetary defense. (oh well, we got this one already
)
4- Standing colonial armies?
5- Colonial policies not only at planetary level, but system level. (I.e. a system could be autonomous within the Empire, or declare independence!)
6- The ability to grant independence to a planet or system.
7- Several kinds of "indenpendence", from autonomy to vassal, to protectorade, to free-trade zone, to really independent.
8- Colonies could be granted the status of Province or State, with representation on the Imperial Senate. (some pre-requistes for this, like pop size and distance from homeworld)
9- Political parties.
10- Elections.
11- Election campaigns.
12- Cheating on elections.
13- Civil War!!!