Gonna do this in parts, as that's a lot to process, haha! Take a deep breath!
Hump-day boredom post.
Fic-wise, I dread to think when I last actually looked at current alleged ME works. I have occasionally updated the profile to say I still intend on completing it but at no particular schedule or time scale. I don't feel like I'm done with it yet but some of the charm has definitely lessened in what I'd intended. There's too many loose ideas in the ether that have yet to fully incorporate themselves into the tale. If I just go straight for the jugular of the tale, there'd be too many "but what happened with.." because I've misjudged laying seeds that I thought would be interesting but with real idea of in what way (again). Ha! Unresolved stuff (not asking for answers particularly, just shooting el breezo):
-should Sha'li (Williams' adopted asari daughter) be Ardat-Yakshi?
Fish in a barrel kind of a sub-plot. I like the idea of exploring Ashley's despair (I think I posted a 'top post short' a long time ago about this) but after that, there's not really much to play with other than continued despair or miracle cure.
Yeah, I can certainly understand growing fatigued with your writing. It's partly why I've taken a break from writing to work on creating wallpapers and comics with XPS. It allows me to keep working on Mass Effect stuff, without actually having to write. Occasionally, I'll poke away at the writing, but I don't think I'll be interested in actually writing a new Mass Effect story anytime soon.
It can be tempting to just finish up the story. That's more or less what I did at certain points with "Paladins" and "Janus." In the former case, I ended up truncating the finale b/c it was just too much to write at that point, and I imagine it'd be just as boring to read as to write (as interesting as some of the ideas were). Overall, I feel the editing made the story more succint, better paced, and improved it. Sure, I missed out on some "red herring" plot points that I might have fleshed out otherwise. However, I feel that this can enhance the writing somewhat, as it leaves the readers wanting more, while still answering the big questions and resolving the key issues, As long as it doesn't get in the way of catharsis, I say do what you need to finish the project, even it is means "going for the jugular."
As for the A-Y subplot: I say use it if you can do something with it. If you can't, and it's just more flagellation of the characters, you might want to leave it aside. That sort of indulgence might be tempting as a writer (and I've felt the call myself), but if it doesn't go anywhere, then it doesn't give anything for the readers to chew. Also, unless you can find a natural method to "cure" Sha'li, I imagine it'll come across as convenient (considering the Genophage cures and whatnot). Conversely, perhaps it's an idea that'll work in another story. I recycle "lost" ideas into future stories all the time!
-if I intend that the Santiago/Massani feud continues somehow via Aria and Councillor Helena Blake (go with it... lol), how the hell does that work out in the context of my story without ridiculousness?
Now, this does sort'a get complicated because it SHOULD have had another sub-plot attached but that got dropped due to the pertaining events being infeasible. Originally, Liara is responsible for Tevos' death who in my AU is Aria's sister, and that would have worked quite nicely. But without that, I'm having trouble coming up with good motivations for Aria beyond assisting the Blue Suns. Liara and Shepard have always been Aria's good friends and allies, and in turn Zaeed is 'protected' but Vido obviously would not see it this way and Zaeed would obviously still rip Vido a new one given the opportunity. The various players have shown their faces but I'm still working on that one... One fleeting mad idea had Aria unwittingly making a deal with the devil (Reapers) to keep Omega but becomes an indoctrinated agent who is able to move freely in and out of the fleet. She wouldn't be the first! lol
As these are side characters, I'd say drop it as well. Again, from my own work, I ran into situations where the side plots were making the story unwieldy and convoluted. However, I also ended up creating an entirely unanticipated side plot that actually bloomed into one of the most important lynchpins of the climax and finale!
However, if you are creating a series of subplots to accommodate something that is ultimately a "throwaway," then I say leave it for another story. Especially if character motivations and such are becoming strained. However, if you have an epiphany, and it improves the story, go for it!
As for those motivations: does Helena still have ties to her old contacts? Perhaps Aria doesn't trust her because of that, and they are always backstabbing each other as a result. Or, maybe they are being misinformed by someone who has a vested interest in seeing them at odds, so they don't focus on this third party...perhaps Vido, or an ally of Vido, who has the trust of either party (or both).
As for the Indoctrination angle, I dunno. A lot of folks (including Shep) have been exposed to Reaper tech without succumbing (although in Shep's case, it's likely due to the Prothean Beacon and Thorian Cipher). Unless you have something interesting going on there, it may weigh you down. Or, you could do what I did and have it be a red herring, haha! I totally had a situation where Shepard's PTSD was supposed to display effects similar to Indoctrination. I was going to leave the answer a mystery until the end. However, the denouement of that particular plot point came near the middle of the story, and ultimately felt like needless torture for Shepard. So I just sort of played that plot point lip service, and moved on.
-is Shepard actually going to become some kind of omnipotent Biotic Goddess?
The last one's difficult. In order for that to happen (it's quite possibly on the cards at face value at the mo), she'd lose Liara. They've been through a hell of a lot in my tales, it just seems like a kick in the teeth - which they feel they've already received their fair share of from the universe. But the 'I am' moment would be fun. I think I can sort of do both... she still has them pesky Reapers to stop after all.
Hmm. I think writing down that Aria arc bit helped somewhat, like what the issues are at least which is helpful. It seems a bit 'easy' to make Blake a 'baddie'; she's pretty ambiguous at the moment though Ashley just doesn't trust her (of course) even though Blake's assisting in the effort to get the Normandy back with the fleet AND Ashley's custody hearing.
See what I mean? Coming back to that lot in media res lol. And yes, I do play the unlikely coincidence game in my fic. 
*gets up off couch*
Is the session done?
Depends on the overall tone you want for your story. It's been a long road, what do you want for your characters? What feels fair? I know life isn't really "fair," but you are the storyteller. Stories don't really have to follow the rules of life. In fact, they often SHOULDN'T. Stories are escapism, after all. I don't mind "the dragon sometimes wins" to be the theme of a 2-hour movie. However, an investment of years (such is in TV series or game series...or book series...ANYTHING series) requires a different consideration. Imagine how you'd have felt if Darth Vader ended up killing Luke in "Return of the Jedi," and Leia fell to the Dark Side. Then Han becomes the leader of the Rebellion, and we witness a space-age "Romeo & Juliet." Interesting story, to be sure, but poor recompense for those people who waited YEARS between films.
All of which is a roundabout way of saying: what do you want your story to say? You are the crafter. There are so many options, so many writers, so many tellings, the possibilities are endless! Perhaps, when Shep becomes this Biotic Goddess, her communion with Liara allows her to retain her individuality, despite "embracing eternity?"
Personally, I always liked to think of Blake as a female Zaeed, and cast her as such in my story, "Project Janus." Moreover, turning her into a baddie would mean one more wrinkle in your Sha'li sub-plot. Which is fine, if that's what's needed to resolve that plot. Or hey, maybe Ashley has to grow as a character, and learn to trust Blake in regards to finding the "cure for A-Y asari."
That's one thing I was always waiting for in Harry Potter: either Draco malfoy becoming the anti-Christ, or Harry having to grow as a character, and swallow his pride, in order to forge an alliance with Draco to save the world. Unfortunately, neither happened, and Draco ends up being a throwaway character, for all that he was supposed to be Harry's foil (as much as Voldemort ever was, moreso even).