Alright, first of all, i'm just a gamer, not a programmer. I know nothin about programming(The only thing i ever did was to change the CSC's stats giving it the manoeverability of the wolfen and 1.5 lightspeed!!! Result- Ship goes faster than lasers!!!

). So, i missed out on some technical points that you said. And secondly, i've played only Trancendence, nothin else(Homeworld or Anacreon).

So, havin a hard time tryin to figure out some of the things.
Anyways, lets get down to business, 1st of all, I like and completely agree with with the fact that it is a mothership and not some hulking destroyer, and hence should have better defence than offence. For a moment, i was carried away by the idea of a massive, super-powerful mothership out to wreak havoc on the badguys.

But that's history now. And, i believe 18% or 15% lightspeed would be enough(The EI500 freighter has 18%). Anything slower would be a bit too slow. And the fact, that the fleet does all the fighting while we defend ourself is good. That's what mothership's generally do. The fleet will guard us and take out the enemy fighters/gunships while the MS(short for mothership) takes on the big guys like Stations/fortresses etc.(Necessary!!! I've lost many wingmen/drones/merceneraies taking on stations, Penitent shrines especially

). And about the defence capabilities, you said '
some good ICX'... If you're thinking about
multiple anti-projectile systems on the ship,
ITS AWESOME! I hadn't thought about this idea. By using multiple ICX systems on the MS, it will be well defended from any type of threat(2/3 Longreach autocannons would be enough to defend this monster). The weapon slots you suggested are good enough for a MS as you said but i'd emphasize on the cybercortex/warfare. I believe, it should have something like this, as in reality, a MS would have such weapons in its arsenal.
The Expandable cargohold system (extra storage bays) that you proposed sounds good but will it be possible to upgrade a 1000ton hold into a 50000ton hold?

I'd like to request you to give it a thought though with the big guys. Max cargo space of 50000tons is good, but upgrading the cargohold at different stations? It's a mothership, generally doesn't need to be upgraded(Just my POV though). And the 'dockscreen magic' concept is good. Will save a lot of programming.
I really liked how you expanded on my ideas. Splitting the Factory bay into Processing and Manufacturing and the Ingot system is awesome. They could be stored as we store ores now and used as and when required. The progress indicator idea is good. And, the fact that research can be started only when an undamaged sample is present on board is novel. I would also like to expand this idea that We could also add a feature that determines the speed of the research.

e.g. Having multiple undamaged sections of stuff on board speeds up research considerably fast(like compounding the time taken). Also, would it be ok if the research would speed up a bit if docked to a station of that type? Like, if we are researching a shield generator and dock at an armour station, or some kind of weapon and dock at a weapons dealer, the research would speed up considerably. Also, if we are trying to research something like the Raisermesser Launcher, and we dock at a raisermesser station or the raisermesser HQ, there is the option of working together with the station to speed up research in return for some favours or the ability to trade research or even the ability to buy the research(from the raisermesser HQ only). What do you say?
The weapons bay idea was for multiple launchers only. I know nothin about the code. Can you ask any of the big guys if this is possible? The reason for this is that its very annoying to constantly keep changing launchers in the game.

The NAMI launcher's versatile, it's missiles are cheap and common, but it's limited to the Lucifer. 75hp tracking thermo works good enough till mid-game, not till endgame(Once, during my early Transcendence days I wanted to see how the Lucifers fared against the Iocrym. So, i bought all the lucifers the game had to offer. It was the most powerful missile i'd discovered till then. With a full payload of 763 lucifers i jumped into Heretic and engaged the Iocrym sentinels... 763 lucifers, 6 sentinels dead!!! THAT'S NOT FAIR!!!

) The NAMI Heavy launcher on the other hand is very uncommon including its missiles, not to forget they're insanely heavy. M2; M5; S3, These are the bad boys, but where do i find them?

If i run out of Lucifers in the small launcher, I atleast have the stilletos, longbows, starburst etc. as backup. But the Heavy launcher? You run out of missiles, get to a station, install a new launcher. Then there's different kinds of launchers- Makayev; Raisermesser; Ares... and none of them are compatible with the other's missiles

Grenades on the other hand are the most commonly found type of projectile that can be fired from a single launcher but are non tracking, heavily inaccurate against(and for) fast ships and very slow/clumsy/dangerous when used in close quarters combat while using a fast gunship(You know what i mean. You're going backwards and you fire a grenade and suddenly accelerate forward to get a clear shot or dodge incoming fire and suddenly you see the grenade's moving slower than you!

KABOOM!!! You got killed by your own grenade!

Happened many times to me.) The everything launcher mod seems good enough for this but, it is very clumsy. You'd have to scroll through a huge no of projectiles to find the right one. So, i had the idea to classify different projectiles as different. So, you could ask Mr. George if its possible. A little bit of dockscreen magic would do...
As for the Building ships in the Hangar, I'd go with a mixture of both the options.

The option could be there to create ships with standard NPC configuration or with custom config. Standard ships would take less time to be built while custom configs would compound the time taken. The more the customisation, the more the time taken. The refit and retire options are cool...
As for the MS fleet ships, if possible, we could add a few new heavy gunships(really powerful ones

) and the rest would be reverse engineered transcendence ships. Also, ship building technology could be traded/bought/looted from different stations and not only from wrecks. eg. docking into a shipyard gives the option of buying researched shiptech. The same way, Looting an enemy station will have the possibility to find researched enemy shiptech like ares ships etc. Also, cruisers and dreadnoughts would be the max size of ships created, CSC's wouldn't look too good being created from a ship. Also, bigger ones like cruisers and dreadnoughts could be built only when docked with a station and not independently. What do you say?
As for your detailed Manufacturing deck, i'd say it's awesome, but it'd be insanely complex to code this thing... and using it would also be quite a challenge. It would be like, you're basically handing out the player to create whatever he wants in this game. Like in age of empires or populous... The coding would be insane for this ship... Using it, even cooler... I can't wait to test this thing out...
PS:- I'd love to hear some more ideas from you...