Good work Triggy, at least your fighting to make Stations usable. While I love the idea, I do think that our earlier comments on 1.0 and 1.1 were pretty much glossed over for 1.2.
Some comments on your drafts.
I like the way that a lot of the standard damage adders have been reduced or removed. Should help keep the damages down. I would also consider making some of the modules reduce the Cores damage (e.g Space Dock and Stealth).
Station Cores: Seem OK at a glance and certainly a big step in the right direction, I'll need to build some bases to see what monsters might fall out
Ancients Base
Command Module: It is definitely not worth the four HPs the second time round. Also, what is the base CQ of the station for the Scout roll. As an idea how would allowing the station to make multiple Scout attempts (max of 1 per ship) sound. e.g. Buy 2 Command modules, get 2 Scout rolls.
Habitation Module: It might be worth upping the damage a little, as this is all the module is for.
Point Defence: Is it really worth adding the interceptors with this since they have been removed from the generic Station Cores.
Hangers: I like the idea of making them less affordable on the small stations. However, instead of increasing the HP costs of the regular hangers, why not reduce the Craft and Carrier complements, it would still means that small stations may have a fighter flight or two.
Weapons: Good work adding more weapons in some of the options lists were pretty light. You just need to make sure that Range/AD and traits balance with the cost (much like you did with the Drakh Neutron cannon and Minbari/ISA Neutron Lasers). In need of attention still, the Narn and EA heavy lasers and perhaps a few others.
Also, I'm in agreement with the others about making less powerful weapons available for less cost - reduce range to normal, reduce ADs etc.
Abbai Interceptors: I'd consider copying the EA for this one. The Abbai are big fans of the technology.
Abbai/Shadow Shields: I'd consider halving the effect and halving the costs to allow them to have an option of being placed on the smaller cores (currently takes up most of a Raid core, though adds a massive boost).
Brakiri: Make Gravatic Lances available?
Centauri Guardian Array: mentions additional interceptor modules, should this read Guardian arrays?
Minbari Stealth Module: Candidate for reducing the damage of a Core
pak'ma'ra: Make Heavy Plasma Modules available?
Vorlon Empire: Add the Advanced Point Defence module (from Minbari)
Planet Killer: Great idea, especially the adding Lumbering. Although when the Vorlons squished planets, they left behind asteroid fields in the show. Also, would a sliding AD scale be better for attacking Moon / Rocky World / Gas Giant?
B5 Battle Station: Your changes mean that a Star Fortress has 27 HP not 24 now. I'd reduce the Habitation modules to 2 (to match the diplomatic Station) and add in a second Interceptor module and a Traffic Control module instead. It feels more B5y.
Was it ever answered if a Shadow Station could be blocked telepathically, or pinned by beams?