I am of the opinion that gleaning the nuances of the economy of economic games is the very essence of the game. What you are asking is tantamount to "tell me everything significant I need to know."
Familiarity will reveal hidden dependencies and subtle bonus conditions....and with a good memory and an eye for observation you will not only be able to describe the mechanics in detail yourself, but play in your way the most efficient was as possible.
There are very few hidden factors in GC2, you can easily make predictions as to how long a project will take, and frequent sliding of the research/social/military sliders will display in real time the precise impact of your changes. There is no mystery, just balance.
That said, here are some tips to help you create an efficent economy...as I have found that credits are the single most important part of the game...as you can rush as many projects as you can afford, creating overwhelming force or impenetrable defense as required.
1) Concentrate on the economy, make it your first priority.
2) Do not expand if you have a negative economy. instead accumulate enough wealth to afford expansion.
3) Build inferior structures even if newer versions are available: they build much much quicker on undeveloped planets and give more bang for the buck and are quick to upgrade....often times you might skip an upgrade level due to rapid research.
4) Each planet is different, do not generalize planets, tailor each planets growth and you will be surprised how much more powerful your empire is.
5) Production Focusing is very useful if by rushing one project, the sebsequent delays in the non focused projects do not actually delay them, if you can subsequently focus the delayed projects..perhaps the focused previous project helps complete the 2nd project. Focusing a factory on a special tile will help build that starship quicker had you focused neither the factory or starship.
6) Factories aren't as useful as you might think: The ability to vary factory output over your empire means your factories are vairable and thusly only a maximum capacity, as you discovered. This requires a more balanced approach and is not disadvantageous since smart research and military production (starbases/miners) augment any potential missing factory structures...also if you like to focus or rush, your factory capacity is deemphasized as a rush job costs the same no matter how many factories you might have.
7) Plan ahead: super projects and racial uniques turn planets into starship powerhouses or research meccas, you have to decide which planet is going to fill which role and accept that your research planet will run deep in the red the whole game, but your financial planet will make enough for both of them, but might not have a starport.
8) React to special tiles and random events, maybe an evil choice gives you a +50% bonus to starships or morale...or you find a +700% tile (yay!) rework your empire around such valuable events.
9) Do not ignore asteroids, starbases or space resources....they are the difference between a stagnant economy and a growing one.
10) Change your style of play, some people have a routine that simply drives them bankrupt, do things differently...choose a different leader, different starting bonuses.
Lastly, CTRL-M... GC2 is so hard at even moderate levels even with diligence I find myself broke and defeated unless I pump funny money into the system....I treat it as a Survey Ship Special. In fact, I can barely beat any Dread Lord scenario without it!