Anvilicious: The bigotry by humans like Udina and Ashley against augmented people despite most other races using them makes the fic come over as this.
Arc Fatigue: Noveria. Even the author was sick of how long it dragged on. For better or worse, part of the reason is that it can really be broken down into three separate sub-arcs, each with their own Genre Shift - the cyberpunk of the Dosadi Arcology, the biological horror of Peak 15 and the supernatural horror of Dosadi redux, with a War Arc overlaying the second and third.
At one point, Udina tells Jensen that there's a chance he might be able to get him allowed back on earth. It seems like Udina is trying to be nice in his own patronizing, dickish way, but a later chapter reveals that Udina plans to have Jensen arrested and handed over to the Order Church the next time he's in Alliance space.
Scholar telling Jules Leng that the latter's "incentive" to go after Adam is "not erasing your whole fucking life" in chapter 31 was douchey enough, but come chapter 36 and The Reveal that Scholar had already erased someone's life in order to make way for "Jules"...
In chapter 47, Adam expresses his concern that the new Executor will replace all C-SEC personnel with robots. In chapter 50 we learn that the person he was talking to is a Snatcher.
The Deep Eyes from Final Fantasy: The Spirits Within were made characters in this fic... then Bioware introduced the CAT6 mercenaries who look suspiciously similar, including the glowing blue helmet optics. Then for even more hilarity, CAT6 shows up itself. As it turns out, Ignus has caught onto the semblance himself - the founder of CAT6 in MEHR was former Deep Eyes.
For all Adam's claimed disdain of Shadowrun on Ilium, he takes to 'running for real like a fish to water in Dosadi.
In chapter 28 an eye-witness misinterprets Adam and co. as "Omars in trenchcoats, wearing fake faces". Guess how Adam ends up disguising himself near the end of the Dosadi arc.
The term technically is Older Than They Think, but the mention of "Forma" in chapter 32 is funny in light of the Warframe influence that starts creeping in later.
Jensen's genetic modifications, which enable him to bond flawlessly with implants, are commented on by Hein; "Maybe he's really secretly the last of the Protheans?" In the game, the Back-Alley Doctor who maintains Jensen's augs finds an entirely new set of experimental implants inside him, and declares, "The shit I found hidden inside you, spliced into your system like that, looks to me like it's from Mars, man!"
Also in the same crossover fanfic Mass Effect Human Revolution, Jensen and his allies have to look for a floppy disk reading machine because some vital information left behind by someone else had been recorded on a floppy disk. In one of the side-missions for Mankind Divided, Jensen recovered a floppy disk containing important data and that requires him to search for a reader machine among the shops in Prague to read the aforementioned data. Of course, Adam still has to tangle with some enemy agents as usual. Coincidence? Or possibly a reference to the crossover fanfiction?
Mankind Divided's Breach mode resembles the same Shadowrun-style cyberspace hacking as in this fic.
The interquel novel is titled Black Light. Blacklight is also the name of an organisation here.
Messiah Creep: Jensen and Co. They may be the only ones with the ability to bring at least momentary salvation to the galaxy. Or they'll die trying to fix the irredeemably broken.
Moral Event Horizon: Jules would have appeared skeevy no matter which way you cut it, but it wasn't until chapter 34 and coming in on the aftermath of his rape-torture of Gianna Parasini that one realises just how messed up.
Nightmare Fuel: "Interludes of madness...". Dear heaven above, EVERY GODDAMNED THING ABOUT "INTERLUDES OF MADNESS".
Paranoia Fuel: Everything about the apparent ease of altering memory can be this. How can you trust anyone to be who they think they are?
The Woobie: Tali comes across as this- you have to be messed up to think that you can't trust policemen. Adam counts as well, judging by some content recently released on Spacebattles.
Even the stuff not on Spacebattles is kinda woobieish: Everything he knows and loves is dead and gone. Family dead because of religious extremists. Can't ever return to earth because of the descendants of said religious extremists. The human government is planning to arrest him to hand him over to the aforementioned extremists. Oh, and whatever good he does is hushed up by the Alliance because of anti-aug sentiment.