You're one of the best game developers on the planet---an accolade that, at this point, is virtually an objective statement of fact (building a custom executable to fix one player's issues, so he could complete his game?  Legendary).  And so, it is with a heavy heart... we need to talk.

These are the facts:  For such a polished, mainstream, flagship title in the 4X genre, Galactic Civilizations 3 is unprecedented in its lack of documentation and cavalier inaccessibility.  The manual is undeserving of the name: critical game mechanics aren't even mentioned, let alone adequately explained.  Other "official" sources, like developer blogs, are plagued with out-of-date information, and require a lot more digging than should be necessary for even the simplest, most fundamental answers.  I had to resort to Google to find out what Population does, and ultimately found the answer on Reddit---not here, where it should be---along with dozens of others asking the very same question.

This may be well and good for some games, where discovery of mechanics is part of the fun.  But a 4X game is no such animal, and GalCiv is not Dwarf Fortress.  Fun discovery in 4X is not about scanning combat logs, vainly wrestling with the math, struggling to cobble together even a vague understanding of something so fundamental as the relationship between attack and defense values.  No, the fun discovery in 4X lies in taking a complex body of mechanics, and finding novel ways to combine them into new tactics and strategies. 

Crucially, that type of discovery can't even begin until players acquire a basic understanding of the fundamental mechanics (at least!)---an understanding you have inexplicably withheld.  Your forums should be filled to bursting with new ideas for fleet compositions, clever adjacency interactions, and module loadouts... instead, we're fumbling in the dark trying to figure out whether Armor vs. Missiles is totally ineffective, negligibly effective, or merely less effective than Point Defences (to give but one example).  The chilling effect on creativity caused by manufactured ignorance is unnecessary and unfortunate.

Below, I've summarized a few of the frustrating questions (those I could recall as I wrote this) that ultimately led to me dropping the game pending the release of adequate documentation---or, to what I would regretfully call your shame, pending the efforts of the community to fill in gaps you should never have left untended in the first place.  (Note:  This thread isn't about answering these questions, but rather to illustrate the startling fact that they exist in the first place.)

• What does Population do?
• What does Tourism do?
• How does combat work? 
• What do combat thrusters do?
• How much worse are "off-type" defenses compared to defenses that match the incoming damage type?
• How do I even begin to decide between a powerful weapon and a weaker weapon that takes advantage of holes in enemy ship defenses?
• What do the symbols in the combat log mean?  How can I learn any of the above when I can't reliably interpret the results of combat? 
• How do Food, Population and Growth bonuses affect races with the "Synthetic" Ability? 
• Are the "Fertile" and "Farmers" Racial Traits entirely useless for Synthetic races?  (Do I effectively have 4 free points to spend in Racial Traits for custom Synthetic races as a result?)
• How do you exploit buildings that benefit ships "built on this planet", when ships aren't built on planets?

This list is by no means exhaustive, and I'm sure many others can think of examples of "egregiously unanswered" questions.  Again, answering these questions (or directing me to developer blogs or other sources) isn't the point of me asking them.  The point is:  These questions should not need to be answered, or even asked.  Such basic game mechanics should be communicated in a tutorial, the manual, or (the best option) an in-game "Galopedia", much like Civilization's exhaustive Civilopedia.

Hopefully something like that is in the works for a patch, DLC or expansion.