[ZeroAdunn]

Ack, don't change cargo storage! The most I would suggest is adding more levels.

Quarian: I think you are wrong about the colonies value. I know I relied on my homeworld for the longest time, but eventually it is just not enough. Also I think that another thing to consider about colonies is that they can eventually become similar to your homeworld (That is the point of the smaller city centers) it just takes a lot longer. And trust me, someone can put up a fight without their homeworld. I have seen the AI move around with fleets of 20+ ships long after their homeworld has been lost. Albiet they were not the best ships in the universe, but they still pose a threat.

I've been using a facility in my games, I don't know if you would be interested in adding it to your game but here is the basic idea:
Slave Mines: Like resource generators but can be built quicker and cause a negetive happiness rate (I believe I heard that you could now use negative values in the mod. happiness perc.)