First off: carrot banana apple and orange , i just wrote 3 pages of stuff down and then accidently deleted it all, well here goes again. 
Some general stuff
Maybe implement advanced figthers that can be researched and then built, which is better. could be a cool addition although a little extra work.
what abouth making the pirate faction out to be a faction completely non planetbased. They cant capture planets nor gain revenue from them, but they can build/capture extractors, and they get their money from destroying .. well everything seeing that the idea is to loot what remains. The trick would be to find the right sweet spot without making them to weak or too overpowered ofc. Could be interesting with a different mechanism for one faction, but it could be a bad idea too ofc. They could still build starbases and have people living there if one wanted for a small income source.
i noticed that the prophet has a very long range on its guns, its a small vessel with minimal firepower, kinda strange that it has that long range on its puls guns. it has almost as long range as the long range missile ship. Maybe a system for weapon ranges could be implemented based on size of ship, weapon type and overall faction concept etc. <shrugs>
maybe change the ravager shipclass to something more appropriate, the others are archangel, watcher,covenant and leviathan. ravager sound so.. nasty. And not like biblical nasty, just nasty.
Lot of fancy religious words you could use for shipclasses: instead of ravager for the siege capitalyou could go with Apocalypse or Armageddon, it fits maybe better with its task, those on the planet must surely think the end has come when orbital bombardment bears down on them. Leviathan is actually from the bible but its also a demon, but i do like that its a religous word, symbolism is good stuff imo.
also the multiply damage abbbility for the ravager class capital sounds a little off. Multiply damage sound like a mathematical term and not an offensive damage abbility belonging to anything but a computer, maybe something for your infocytes. 
What abouth purgatory, purgation or divine wrath instead.
also a general comment, maybe not give shield piercing missiles to every faction, that should maybe betech reserved for the more technically advanced factions or just some it fits well for.
Another idea: why dont you make the "super cannons" more diverse, normally its just either spread culture or do damage, what abouth making the plague's infect a planet with a long duration plague that slowly does nasty stuff to a population, also dont let it be a typical cannon that fires something, its better off beeing a normal structure, you could call it infected laboratory or something entirely different and do the abbility something like "tailored viral attack" "The plague creates a nasty virus designed specially for the designated population on the planet" something like that. The effect could be anything you want, from halting regen of population to killing it fast/slow or decresse max pop. I would make it halt regen completely, and do a small amount of damage but over a long time, so at the end of the duration the population would be either dead or close to death.
the rephaim missile ship is one strange bird among the other ships, intentional or?
The others all share a certain estetique, but this seems like something belonging to a diff faction. well atleast somewhat. i can see a line here and there that fits in a little.
bit more specific stuff:
decay hull research reads: adds azid weapon to all turret (missing an "S")
locust swarm abbility on the carrier cap is vague on what it does, "calls forth a swarm of missiles that target every enemy within range" yet i see no range indicator for it, nor is any stats such as damage listed. maybe change this abbility to fit the text or change the text to fit the abbility or just clear up the text depending on which option it is hehe.
seraphim defender gets destruction abbility, templar elite gets immunity, but in the research it says it should be reversed. Immunity should go to defender and vica versa.
the weapon uppgrade divine force says only two capitol ships are affected but that is wrong i checked and it also affected the convenant and its plasma weaponry. it also affected weapon platforms which is not listed either. Just clean up what it affects in the text i reckon or change the description to a general sentence and no specifics.
the colonice battleship is called convenant, is it meant to be covenant? i suggest covenant myself as one of its interpretations is a biblical contract between god and hes followers.
the obscure strikecraft and diminish strikecraft research dont say what its for, it am guessing itperhaps attaches to the hangar since it is a direct line from that researchbut when i research ity idont see any abbility etc pop up anywhere, change the tooltext to state what it actually does and if its not there fix that.
the purifed missile research upgrade reads purifed missles.
the starbase uppgrade infect planet has a gramatical error it reads the vampires on the star base create entrance... me thinks its one word to many there.
infected beam blast a power belonging to the invictus cap ship reads: all targets within a column are consumed by the path of the infected beam blast. Rather strange sentence me thinks, maybe change it too: all targets within a column are consumed by the(power) infected beam blast or change it entrirely to something like:a powerfull ray of corrupt energy sweeps lesser ships away and severaly damages more powerful ones. or whatnot, i could come up with 100 sentences but meh, its your mod i dont presume to tell you what to write.
molecualr bonding abbility belonging to the same ship misses a D in its description after ..resulting in increase"d"
This second attempt got a little messy and was def shorter, but hey, still got down a few lines. Sorry for any bad spelling or bad language.
