Primary/Secondary (Ship) Weapon Mounts and Weapons types are mixed up
Atrocities :
I have given due consideration to this issue and while I fully understand your point of view, and agree with it, have decided that it would require to much work and effort to change at this point in time.
I can understand that.
I had to go back to my original notes from way way back and in those notes I found that I had chosen to use pulse weapons as secondary weapons because the intermittent beams were used by many sci-fi shows such as BSG, Buck Rogers, Star Wars, and such in an anti-fighter way. Also people wanted pulse weapons and I had to come up with a way to make them useful in the mod. Also sustained beams, in star trek and other shows, have been historically used as the POWER weapon. Since they only fired a single beam, they were not efficient enough to be used for targeting smaller objects.
Concerning Star Trek, IMHO and AFIAK you're wrong: There are very few pulse weapons. And those are used to punch through heavy shielding, not spray some "area" of space to hit a strafing fighter-bombers, pardon: space fighters. Even small targets like shuttles or fighters are generally fired at with beam weapons. I can't even remember seeing a real PD weapon once ... Examples are Defiant (4x Type-U pulse phasors mounted with very limited forward firing arc) and (nearly) all other "modern" federation or cardassian vessels which mount large-array beam weapons with wide firing arc. Those are deployed against all targets.
AI designs "Explorers", but does not build them or uses them when build by player intervention.
Atrocities :
I can only give the AI the instruction to have these on hand, whether or not the AI actually uses them is up to the AI.
I must correct my statement: SOME AIs seem to be unable to build/use explorer class vessels. Points to some error in their files ...
I must correct myself even more: "Explorer" is in reality "Attack Base" .. and are still build as if they where costly bases, not small exploration vessels: in infrastructure mode, on defense, attack etc. but not in exploration mode.
Armors with "hit first" ability should scale to the size of the vessel, as they effectivly must be covering it completely.
Atrocities :
I don't understand what you mean by this.
Standard armor is not longer flagged "Damaged before anything else" and is practically only a sturdy component without any further function. Some racial armor still prevents hits to other components (is not "leaky"). With propulsion and shield systems scaling to the size of the vessel, these armor components should scale to size as well, because they must be covering the entire hull effectivly.
Proportion mod has these scaling armors IIRC.
Monsters should have "plague bomb(s)/ability, or ground troops"
Atrocities :
Monster don't have troops or at least I don't believe they do.
Exactly. I would like to see them invade planets or kill of the pop using biological means. (guess it would only depend on the size of the parasites if its a plague or an invasion
)
Sheliak (1.9.7.3)
Description says "are suited to very hot environments and they die quickly in cold". They get "Rock Planet Colonization - Rock Natives" Tech.
Yet they start on "Hydrogen/Ice" planet? (What really seems to irritate the AI ... somehow managed to colonize 2 rock planets in its home system with its colonizer still listed as prototype ... while 2 other rocks where left untouched. And 3 ice planets, because the colonizing tech missing)
Code:
Sheliak_AI_General.txt
=============================================
AI DATA FILE - Sheliak
=============================================
Name := Sheliak Morbid
Biological Description := The Sheliak are a non-humanoid
species with 4 arms, and 6 eyes. Their bodies are suited to very hot
environments ...
Planet Type := Ice
Atmosphere := Hydrogen
.. I would like to suggest Rock/Methane ..
Breen (1.9.7.3)
Build ships without "Impulse Engine", therefore with very low supply capacity - they're running out of supplies before even leaving their home system. "Organic Nacelle" triggers the "engine counter" - whos max is e.g. 2 for the DD hull, yet the AI puts in 6 nacelles, and no impulse engine.
Colony Ships and Explorers are build correctly, attack, defense ships, troop and pop transports are not.
8472 builds "correct" ships, btw., bespite using organic tech as well.
Code:
Misc Ability 3 Name := Combat Movement
Misc Ability 3 Spaces Per One := 100
.. should be (at least it work if I change it that way) ..
Code:
AI Tag 05 Impulse Engines
Misc Ability 3 Name := AI Tag 05
Misc Ability 3 Spaces Per One := 100
Strange thing is - some races construction templates seem to work with "combat movement", while other seem to need "tag 05" .. guess you've mixed up both somewhere in the racial techs/files. Good luck getting that straight 
Propulsion Experts (1.9.7.3)
.. get +2 movement, but trait description still says +1.
+2 is too much, anyway.
Monsters (1.9.7.3)
Name := Monster Drone
Short Name := Monster Drone
Description := Monster Base used by the monster as a base in space.
"Monster Yard" .. "can repair 20omponents" ..
"Monster PD 1" .. 200kt ?!
Build "Base Space Yard" without "Monster Yard" and "Monster Cloak".
Btw., how is "Monster Cloak" supposed to work, anyway.. haven't seen any cloaking effect from it?!
Pirate Races
.. should get special boarding troop from turn 1 ..
Re: The Star Trek Mod - v1.9.7.3 *NEW*
I doubt that I will update STM for a while though. I am working on the Star Wars Mod right now, but I have put your issue into "My Things To Work On" list. Thank you for them. 
Linear Mode
