So here's a lot of food for thought.
4d facility - energy Biology lab Progenitor Psych
I don't buy this one at all. Xenobiology is
not the Alien's story. It's Deirdre's. I can understand using it here if you wish, but to declare it an ironclad hard association, that's just wrong. Doesn't fit with the game's lore.
Myself, I've ended up assigning this to Biogenetics. It's biology. However, I've also at times used Biogenetics as my Police State technology. It has a relevant quote / voice acting from Chairman Yang. "We hold life to be sacred..." Over time, using Biogenetics as my Discover 1 tech with a Biology Lab, won out.
2 ability Hypnotic trance Secrets of the Human Brain
It's of course not wrong to do that, but there are other places you could do it. I've done it in Progenitor Psych and Centauri Empathy. Currently I've welded the Virtual World to Secrets in the Human Brain. I think that's a good lore fit. I've done the Virtual World elsewhere though, like Optical Computers.
4a facility - military Perimeter defense Doctrine: Loyalty
This is one of those cases of "familiarity with the stock game". There's no inherent relationship between between loyalty and a defensive wall. One could
imagine a relationship, such as keeping people
inside, but that's not really what a Perimeter Defense implies. I decided a Perimeter Defense is a kind of armor, for cities, and gave it at the same time as I give Plasma armor.
4b facility - drones Hologram theatre Polymorphic Software
I don't see any inherent relationship between these ideas at all.
4c facility - misc Children's creche Ethical Calculus
Another "familiarity with the stock game", not inherent.
1 unit types Mind Worms Centauri Empathy
Not wrong, but I repurposed Centauri Genetics from later on.
1 unit types Spore Launcher Bioadaptive Resonance
I guess you don't have 3-Res armor. I do, so I just gave Spore Launcher at the same time as mindworm. I don't see a good reason to give them out in different techs.
4j facility - size limit Hab complex Industrial Automation
This is stock game familiarity, and not inherent.
6 secret project The Virtual World Planetary Networks
A reasonable idea, and I've probably done it. However, I use this for probe teams and Police State. Chairman Yang is watching you!
1 unit types AAA Tracking Advanced Military Algorithms
I put it in Doctrine: Air Power. I don't believe that anyone should get "a chance" to prepare for Needlejets. That chassis is substantially more expensive in my mod anyways. The AI doesn't send them out like flies.
3 terraforming Thermocline transducer Adaptive Economics
Although there can be a relationship, I just don't see it as inherent or exclusive. I want Adaptive Economics for my Socialist. I think it's the obvious place for Planned as well.
6 secret project The Planetary Datalinks Cyberethics
It's stock game familiarity. It doesn't actually make any sense at all. Hasn't made sense in my mod lately either. Cyberethics doesn't have much to do with anything!
4f facility - minerals Genejack factory Retroviral Engineering
Not wrong, but I did Bio-Engineering.
6 secret project The Citizens' Defense Force Intellectual Integrity
More stock game familiarity. Makes no actual sense at all. The quote / voice acting is Zhakarov talking about what people prefer to be true, rather than what the evidence shows to be likely or possible. Just isn't relevant to survival militias patrolling perimeters. I repurposed I.I. as a Discover tech. Like I'm guessing it probably
was at some point in their development. There are some clues that they had some rebalancing troubles, like Optical Computers not doing anything.
7 weapon Fusion laser 6 Organic Superlubricant
Familiarity; doesn't actually make any basic sense. I repurposed it as the basis for hovertanks.
4e facility - ecodamage Hybrid forest Planetary Economics
Ask yourself why this would really have anything to do with trees.
1 unit types Hovertank chassis Nanominiaturization
Again, why. Nanites magically float things because...?
2 ability Carrier deck Nanometallurgy
Never made a damn lick of sense, and was clearly mapping a Civ II military progression into SMAC. Totally inappropriate, we're not making a transition from battleships to aircraft carriers. I put it in Doctrine: Air Power, even though it makes that tech a bit overloaded.
4h facility - prototypes Skunkworks Advanced Subatomic Theory
Doesn't matter that much where you put this. I put it with Neural Grafting, which is still when you get 2 abilities in my mod.
1 unit types Copter chassis Mind/Machine Interface
Never made one lick of sense. It's just a military progression.
4a facility - military Flechette defense system N-Space Compression
Flechettes are small darts. Doesn't have anything to do with compressing anything.
4b facility - drones Paradise garden Sentient Econometrics
Why? Is the garden made out of robots or artificial intelligences? Out of money and businesspeople?