I agree 2 had a better economic system.

True indeed, something like GCII's economy should be implemented. But some of the changes they have made now (indexing Total Production to population, for example) are rather beneficial. I envision the system working something like this:

1. Population should contribute to Raw Production, which can be added to by various buildings. This Total Production would be split into three categories:
1. Manufacturing (certain percentage of Raw Production * modifiers from factories, etc.)
2. Services (certain percentage of Raw Production * modifiers from Market Center line, etc.)
3. Research (certain percentage of Raw Production * modifiers from Research Lab, etc.); research for the private sector should slowly increase the Manufacturing and Services output
2. In each sector of production mentioned above there would be certain fixed costs of maintenance associated with buildings, and variable costs associated with labor (i. e. Raw Production put into each of the sectors, which would be quadratic). Meanwhile, each unit of production would gain only 1 BC of "revenue" for that sector, although Market Centers would have a double effect of increasing both services output and the amount of revenue gained per unit of sectoral production ("Economy" bonuses would be applied to revenue gained.). Based on these factors, each sector would attempt to maximize profits. The formulae given above would only represent maximum capacity which may or may not not be economically optimal for a sector of the economy. 
1. Manufacturing sector would have low fixed costs and moderate variable costs.
2. Services sector would have medium fixed costs and low variable costs.
3. Research sector would have high fixed costs and high variable costs.
3. The overall economy should be optimized to maximize profitability. As mentioned earlier this may involve not running certain sectors at full capacity, and Raw Production itself can be generated directly by buildings or because of modifiers from Interstellar Governance, Hives, etc. In both cases, the amount of population needed to reach maximum overall profitability would be reduced (i. e. unemployment, more on that later), although in the latter case the effect would be counteracted by the decreased cost per unit of total production, proportionally. (reduction by the square of increase, times the increase to account for wage growth, leading to a linear proportion)
4. Based on the productivity at a profit-maximizing level, a GDP figure (sum of manufacturing + services + research) and a profit figure (profits in each sector) should be devised. The player should be able to set a tax rate on profits from 0 to 100%. Morale should be multiplied by a factor equal to (1 - tax rate)(1 - unemployment rate).
5. Economic planning should also be possible; the human player 
6. Taxed income can be used by the player in order to operate factories and research facilities for Manufacturing (Social/Military) and Research, continuing on the same cost curve. Of course there would be other uses like ship maintenance for the money which would follow a cost curve of their own.

It may seem complex, but for the player it won't be all that difficult. It will, however, be far more interesting than the current system, especially when political parties are added that can affect the budget.