Aye having the rogues do less planetary destruction and resettlement and more stealing and plundering can only be good, so go ahead with the siege type cash farmer.
Might aswell remove all their siege abbility well except for the caps i guess, and instead give them raid vessels that act as siege but steal instead of loot. Would change the faction nicely more into pirates because instead of seeing common spam of 5-6 vessels trying to bombard your planet into dust you would get pirate raiders trying to get rich. The emperor approves of this. If it were up to me id like an entirely new approach to taking planets for rogues but that is too hard, and having some abbility for planetary bombardment is not too out of character for the rogues i think, i can see scenarios where they would do it so letting the caps keep that abbility should work out nicely.
Yeah i see why you want a meteor for the hangar. hehe.
So the rogues are good then? You got enough ideas to toy with there i reckon, or you want more? I reckon one frigate that acts as a mobile hacking platform with the mentioned abbilities should do nicely for a utility frig, and then the changing of siege vessels to raid vessels, and why not make a fire ship?
i see 2 possibly versions of it: one where it has really low hp and are slow but its explosion are fairly large and do big damage, in this case the ship should actually be able to be shot down before it gets close and explodes.
The other version would be the exact opposite and act more like a mine as you described it. I personally think i would prefer the slow big explosion, it would be a real piratish improvisation, fill up the oldest crappiest barge you got with whatever cheap soap-explosives and aim it at the enemy fleet and activate its autopilot (or tie the rudder and aim it in the genral direction:P)
I like that you have a psionic tree for hypercorp, it makes them stand out more, just try to steer them in a different direction than advent maybe so they wont be too similiar. Good idea though, The emperor approves. 
Transhuman science: Morphs? i assume this is the standard pop increase for the mentioned terrain? Morphs hmm, interesting name, what made you choose morphs? I would think terraforming would come easier to mind.
Anyway you gave me something to work with with the trees, ill sit down and think abouth some abbilities for utility cruiser and starbase abbilities for hypercorp.
And whenever you have something that needs proofreading ill be happy to look it over.
By the way i looked real quick over the rogue cap ships abbility descriptions right now and there are still stuff to do!
Cobra destroyer: reads:"...the captain clears out redundant lifesupport systems in favour of redundant repair systems" Change this to "...the captain clears out redundant lifesupport systems in favour of more repair systems" or "...the captain clears out redundant lifesupport systems and instead installs more defenses. Or whatnot. 
Berzerk charge:Change to this maybe: supercharging their engines, the ship achieves a speed and acceleration that would kill an unaugmented human.
vipers kiss: The enhanced crew knows just where to place their shots to cripple enemy defences. i know you wanted to put in something related to their cyber-nature, but enhanced instead of experienced here do sound a little odd, or is it just me? Your call ofc i am just saying it as i see it.
Rogue Barrage: this def needs a new name, to put things in perspective: imagine an american general standing in hes bunker calling out "FIRE THE AMERICAN BARRAGE" and then comes from the sideline another voice "FIRE THE BRITISH SALVO" and then "FIRE THE GERMAN BOMBS", "CLEAN THE FRENCH TOILETS" etc lol. Dont say you dont agree with me. 
Green arcadia:Raid ports: it reads despatches, shoudent it be dispatches? My poor english says it should. But you can slap me if im wrong.
last man standing: instead of "when called upon" which sound like your calling for a butler maybe use "when activated".
Ghost: the "Ion bolt" abbility could maybe be changed to "Ion Cannon" and the text as it is now is: "ion disables the targeted unit, preventing it from moving or attacking" what abouth dooing: "The ion cannon disables the targeted unit, preventing it from moving or attacking for a short duration" OR "Firing the ion cannon at an enemy vessel, the enemy are left totally helpless for a short while". Or whatever you want, just put something before "ion disables" 
AnnaV: mighty shot: Maybe change name, based on its description it is a missile attack, and mighty shot sounds like a cannon, can use "Missile strike/Rocket strike", "Missile salvo/Rocket Salvo" instwad i guess, seeing it is a missile attack that can hurt several along a path it neccecitates several missiles so salvo should be the most accurate.
rapid reload: Seeing this affects every ship in a radius and the description says something abouth it beeing done to impress the capt'n, wouldent inspiring presence be a much better name? 
Lol some nitpicking here. I am fond of that, but you dont have to answer, i am just reminding you incase you have forgotten and trying to push my views on you like a used car salesman. 
edit: discovered a bug with the nephilim. The starbase uppgrade module mass reverence can be purchased to lvl 2, but when you buy rank 2 the visible stats stay the same as lvl 1 and it is still listed as lvl 1. I dont know if it actually changes, but it looks like it dont.
: Discovered another possibly bug, the nephilim research bliss->faith->healing has 2 levels and when i buy the first i notice all my structures and ships in the viscinity of the holy shrine gain 1.5 point of hull repaired/sec, but when i purchase rank 2 it stays at 1.5 and i dont see any change. Maybe it gives something that is not visible but i just thought id let you know just incase.
: came across two names for plague cap ships that i thought sounded a mite off: pluto and osiris. I know pluto is a different name for hades but it was used when speaking of the underworld in a positive matter, and well, the plague is anything but positive, and osiris wasnt in any way seem as evil so i found the names a bit strange.
Im adding a few fitting mythical evil names incase you feel the urge to replace some, if you want the meaning aswell just let me know:
Abbadon, Demogorgon, Lamia, Nergal, Apep, Dagon, Kali, Leviathan, Mammon, Malphas, Moloch, Orcus, Morana.
: the invictus class cap ship has an abbility called retaliation, it is a damage shield, Why does this not show the duration of the effect? I have noticed that in other mods aswell. This type of abbility never shows duration. Its kinda annoying not knowing how long it lasts. Is this some hardcoded bull in the engine or something perhaps?
: the plague blood hunter vessel has two abbilities that can be researched, one work just fine because it requires no matter but the other requires matter and therein lies the problem, because the blood hunter got zero matter.
: regarding the biochemical receptor growth research is it only supposed to affect cap ships, the previous 3 researches in the same tree each added a stacking 10% to various areas for both frigs, buildings and caps but the 4 research biochemical growth research only seem to give the last 10% to cap ships, is this intentional or a bug?
: i also came up with an abbility for hypercorp: Clone/cloning center/Cloning lab/cloning facility/whatever:it can be an abbility for a cap ship or for a structure/starbase. The corporation clones its most valuable employees so as to not loose their service should an untimely death occur. This way, when a skilled captain is killed in battle, the corporation can bring him back to continue hes job. This will be like the ressurection abbility of the advent in effect, target a ship and give it the higher level of a deseased crew. (if that is how that ability works, ive kinda forgotten)
: besides that i kept thinking that a hypercorp should have some financial research aka, stock market, stock manipulation, corporate payout etc, just take the terms from the corporations of today and wall street i guess, they are as corrupt as they come, i just had to say that. 
: Meh, bad news, the hypercorp still ctd's when you manually click on the crystal extractor, note it only does so on the crystal extractor, not the metal extractor. You can build them from the planetary build meny just fine but the crystal extractor is no-no manually. My appolgies for the mistake when i reported it fixed, i must have failed to check what extractor i was clicking on.