Now, does this really mean "star system", or does it mean "individual planet"? For instance, if Earth is really rich, and Mars is really poor, but Mars creates a freighter, will it reap the same bonuses as a freighter built on Earth?
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It is indeed the Star System that is important, not the individual planet. Trade routes operate off the economy level of the two endpoint systems, the distance between them, each participant's Trade ability rating, and Trade improving starbases.
The distance and the Trade rating/starbases are mulplicative factors, so they tend to contribute the greatest effect on a route, but they still require a viable economy on both endpoints to work.
Generally speaking, social improvements (including Capitals) affect the planet only, apart from Trade Goods and Galactic Wonders, which give a bonus to your entire race
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And influence/culture_resistance improvements, which operate at the star system level.
~SDC~