I finally have enough of a handle on what I think is going on here conceptually to warrant me creating a post. Hopefully Frogboy will glance at this so I'll strive for brevity.
In regard to the tech costs increasing, I call it "scaling" which is a doubling of the research cost of weapon and invasion technologies. Nothing else scales, including defense, which I found interesting.
It appears to happen to all races, so it is not tech tree-specific. Nor is it specific to a particular branch or piece of tech. My first few observations of scaling occurred after researching factory techs, so initially I believed that caused it. But I was incorrect. Scaling can also happen multiple times to the same race in the same game, which is why this problem is so noticable and game-changing.
What I believe causes scaling is something in the code that says essentially this: When a player (person or AI) has researched far enough along in 1 or more tech branches, the game figures that this player's infrastructure and total tech level is sufficient for a fairness balance to occur, and this balance is the scaling of their weapon and invasion technologies.
This explains why some AI appear to act so strangely. Scaling can boost the costs to levels that prohibit any competitive or even "barely keeping up" offensive research. I observed the Terrans fairly early on with Industrial Centers and a fair amount of other tech, yet zero weaponry. I got my spy info level to advanced and saw they had no weapon or invasion techs. In my experience, Terrans and Thalans suffer from this most often, but I've seen Altarians, Arcean, Yor, and Drengin(once) to varying degrees as well, though much less often.
I do not see this behavior in the Torians or Korath, and though I believe the problem affects them, they must somehow reduce its impact by their AI behavior, perhaps due to their leader personality and how they pick techs to research.
Races that seem to "spread it around", meaning tech diversification, appear to suffer most from this. However, those that stick to 1 or 2 branches appear far less affected, although I'd wager they still take a hit now and then. The instances of races building lots of defenseless ships is the AI knowing it has to build ships and acting on it, yet not having any weaponry to equip due to scaling problems.
I have save games showing scaling. I have some before and after files because I have no idea what shows up in a save file that could be found useful. I don't think I can use smart exception because the game does not crash.