Check your expansion planner (second button on the left of the top menu bar). If you have a greater demand for any resource than you have as a stockpile, then you have a bottleneck. (If it is a luxury good, it is just reducing your potential income, not creating a building bottleneck.) Also, if you have a decent stockpile, but due to overall galactic demand, the price of that good has been bid up beyond the minimum price, it will increase the maintenance costs of all your ships and bases, so you'll probably want to build more mines for that resource, just to mitigate the effect on your own costs. If you have no stockpile shortages and both your State and civilian economies have a decent positive cash flow, then your economy is doing just fine.
> Is it possible to let the AI manage civilian ship design while I handle military ship design?
Yes, check the "research and design" section of your "Empire Policy Screen" (forth button from the left in the top menu bar).
< Message edited by Panpiper -- 8/30/2012 8:33:34 AM >