Do ships have people in them?
I believe that there is only 1 person in the game and that is YOU.
No seriously, 1 person in the home command station on a computer controlling all the ships with tactics, just as you would.
Everything else is robots that do things by themselves. ex: spacedocks uses machines that follow an specific order so that they only create things, they don't "think".
( I believe AI is just a more complicated response system. ex: if this happens, then we do that, only "this" has a few infinite possibilities and robots has only a few possibilities)
Why do we have ship caps?
I believe that YOU the commander has a bad computer that can't handle so much processing( can't control that many ships at once)
What is knowledge?
I believe knowledge is "time" we can start researching things, though this "time" needs new information to actually "invent" or "discover" new things. What's in the knowledge i suppose it's physics and engineering new skills( which is why i believe that if you parasite a ship, you can research it and capture that technology)
How do we know what we can unlock?
I believe we either have a psychic commander, or we seen this type in the ai, and we know the basic information about it.
Why don't we need plutonium for nukes?
To answer that, you must understand we can just use a lot of metal and crystal to make nuclear fission or fusion happen.
my serious answer is we use hydrogen or anti matter for super explosions.
Why is there co op?
Cause you have some pal that wants to have some fun, so you , the commander decides that you will let your friend destroy your whole army by nuking you and by creating alliances with the ai,
Why can't we upgrade our ships when we are finish building it?
upgrading requires way way too much time compared to just building an mk 2 or 3