Congratulations on finishing this fine story Paranoid
I hope you feel some pride in the accomplishment cause you've done well and it's very worthy of the reading.
My impressions;
Again, overall it's an in-depth and interesting story with fully fleshed out characters that the readers (imo) can sympathise and feel for. With lots of plot twists and unexpected events to spice the arc up and events that left me wanting the next chapter.. now dammit

. <- which is the sign of a decently written and engaging story that sucks the reader in. Again well done.
BTW if you like writing, maybe you should try some short stories (not necessarily game related) and join a writers club to expand you art. I know where I live some community radios had a late night segments where novelettes are read out over the radio, Maybe there's something like that near you?
For the story overall, before any re-writes and fix-ups..
An interesting take on the game, different and thoughtful, maybe a little above what the games core was, but creative none the less. It had characters and events that felt in-line with what they should have felt/done.
Sometimes the writing was heavy and could have been trimmed a bit in the choice of wording but overall it didn't detract from what was there in the plot & particular scenes.
Sometimes I felt there was a sudden plot-jump into a sub/side-plot that had little warning or build-up. This felt a bit like a "skip" on a CD or DVD that just jumps into a new scene and I'm left wondering how it got there.
That isn't to say the side/sub-plot was bad, just a little more explanation on events could have helped.
a brief notes on some of the specific points you wanted.
The Prologue:
As you noted the prologue felt different than the main story arc. To me it feels like short story set in the same universe but different from the Main plot. (The 1st Act upto the Hammer incident has some of this feel too. Maybe because the plot then goes into Corealien/Tur Ryn territory and away from just events in the X-universe).
my suggestion would be to try and have the garrin intro tie into later events. (maybe have the pirates he fled from meet him at a later date and re-act/interact some. Cause as far as I'm aware the pirates just end up Damned and he never see's them again, so that makes the intro feel a little like a "fluff piece")
Trim repetition:
Maybe not re-explaining some of the previous plot events. Although maybe that was more of a symptom of you writing the chapters one at a time, with time between them. And when finalised into a main (1 off) story they can be removed without damaging the flow of events. That's something you'll have to trim and see how it looks when you do your re-edit.
Chapter Length:
Nothing really wrong with them atm. Here on the forum boards they might seem too large, but when they all get compiled into a book/pdf format they'll seem more suited. Maybe a merging of some like events into a chapter here and there but overall they're Ok.
Label Consistency:
we talk about this before and you're aware of what I think
Missed Typos / Dodgy Grammar:
Yes there are some

, but once you can get it into a single file PM me and I will help you if you desire it
Window Dressing:
If you want more then ok, I felt things like Amon on the Split planet with the Robot Warrior were good for this, but as said above, make sure you give some description on how events got there, don't just "Jump" there.
Character consistency and uniqueness:
You've done well on this with the major characters, maybe some need some more fleshing out (Elaen with Ravn, especially later on [for example]). And check that not all the Pirates/Dogs are clone-like and have different reasons for who they are and what/how they do things. But they're your characters so I won't like to advise on how they should be..
Inverted Commas;
Yes, most obvious
A little less waffle:
what, where

, points to this post

.
A little suggestion for multiple naming for certain characters....
If you want to break up the naming counts for some characters, a good way to do it, is to name people by the different people they interact with:
ie: Tur Ryn can be known as "The Devil" when he's with his own pirates, as "Bane" by Fey, and as Tur Ryn by Jess/Kerry and people who don’t know him as either and Ex-pirate of the remade Devil.
Again Fey can be with the professor and Ban Danna and Faith can be with the legion.
Something for you to think about at least.
Again congrats of finishing the story, I enjoyed reading it immensely and consider it one of the top X-universe fan-fics
Now take a break, but please don't let the skills fade, write a short story or two. (Doesn't have to be in the same game universe you've set, maybe try something different)
Thanks for taking me on this journey into your world.
Snowship
And now that I wont dilute the different stories in my head I can read others..
Sometimes its hard to keep track of different stories when your reading multiple ones. I know it's like that with me atm. Reading this, an e-book at work during lunch and a different paperback at home... sometimes they just blend with one another
Damn this's a long post...