Here are some thoughts on integration of the three:
1) A race with a commercial advantage ought to get a bigger bonus from trade (as in the past)
2) However, at a certain point, not only should they get an advantage, but it is a drain on the race they are trading with. Think of the Italian city states vis a vis the Byzantine Empire of the Middle Ages. They developed such a commercial advantage that they sucked the empire dry. Or the Western nations vs. 19th century China. Not to get too political but look at what is happening today with certain countries. Non-trading races should not do well when it comes to trade - there some be something like a trade deficit impact (as in the US vs. China today).
3) The advantage shouldn't happen all at once - at the beginning trade will be good for everyone but it should get better/worse over time (depending upon who you are in this relationship). So at first everyone wants/needs to trade, but that outlook changes as time goes by.
4) There should be diplomatic penalty when a race gets a certain amount of trading advantage over another race. It should be harder to keep good relations with them. You should have to do more things (give technology, money, military aid) to keep them pacified. You also want to do this in order to continue to reap the benefits of your positive trade balance.
5) There should be certain resources that play a role, much like oil today, in the game. And possession of those resource should give a race an advantage, either trade or military or research or socially, etc. They would also provide something to fight over. Race X finds World Y with resource Z - and Race A wants it! Rather than just planets, we should be struggling (through diplomacy or war) over resources. I'm not sure I like the Civ3 way of having to have oil in order to build tanks, but maybe there is a technological end around if you don't have a resource, or you are just weaker in a certain area if you don't have it. This would add a layer of depth to the game. Also if we have minor races again, resources could make them more important, much as Kuwait today is more important than it's size and population would otherwise say.
6) Resources might also be a way to offset a trading deficit. If you are up against a good trader but have a resource he wants/needs, it would help offset your trade deficit, much like the oil countries use oil to buy other things they couldn't otherwise afford. Technology might also be a factor. The greater the difference between your tech level and the trader, the less the impact of the trade deficit as he wants more of your high tech goods.
Lots of potential angles here. Just some thoughts, if anyone has already come up wtih these, apologies.
