I actually think the trading system, as it stands, is pretty good. Money is generated per trade good, which is a fixed tonnage (if memory serves). So changing civilian mine production to alse be based on tonnage would be a nice change. It does make more sense too.
Or perhaps even a symbiosis of both. Each civilian complex produces a base of 30-50 weath (representing income tax on wages, increasing use of taxed supplies in the empire, possible mining rights etc), with a produced tonnage based formula added on top of that so that a good mine produces perhaps 150 weath total, and a poor mine 100 wealth total.
This way, the algorithm for generating civilian complexes need not be changed to retain balance. Even several poorly producing complexes would not ruin a game, while several good complexes would not be a game-breaking boost to economy.
Also, at the same time, cost of purchasing the minerals from that mine could easily be changed to match the new formula. Keep it at double the wealth production of the mine and it all balances out.
Of course, this would require some changes to the civilian tab of the Production window, as it would need to display the calculated wealth production instead of the fixed text.