As our audience is constantly growing, I've decided to gather some basic information about the series in one place, for easier access. Hope this helps to shed some light on how I approached the whole thing and what you should be looking forward to. Also, big thanks to whomever used the term "MScanon" first - seen it previously on the net.

If you'd like to know more about the Marauder Shields project, be sure to read these two interviews as well:
Gamefront: [link]NewGamerNation: [link]Consider the comments section underneath this image as a great place to ask questions that you think should make it onto our FAQ article!

Also, general discussion and opinions are always welcome!
Mass Effect stopped at ME2.
Luckilly, we have koobs to finish the story for us!
Thank you for giving us back ME3.
However, right here you state that the Citadel isn't the Catalyst, as Shepard believes. That completely goes against what the game establishes before the ending. Simply saying "oh, Vendetta is wrong" doesn't cut it.
I can't help but to be amused at the "Plotholes" disclaimer. I can only read it as "if there's a plothole, I'm going to handwave it later." I am quite cynical, but that's not good writing: if something contradicts what I've been informed of, then I expect an explanation promptly. I'm not going to wait long for the author to give an excuse.
I am actually going to mention the fate of the Protheans again later on, I'm just telling you here and now: Vendetta operating on insufficient data - the one gathered by the fallen Protheans - *IS* sufficient, both here and in Mass Effect 3, it is a fairly standard storytelling technique that works now in the same way it has worked for ages. You know, in the time period that jaded negativity (a.k.a. post-Greek cynicism) wasn't being promoted in the contemporary culture as something "cool", when being self-classified as a "cynic" was announcing that you are not to be reasoned with, that you're intentionally excluding yourself from the audience/discussion/show/cultural life taking place at a selected venue. Just sayin'.
The plotholes disclaimer isn't there for your amusement, I assure you. I've put it there because some of the readers (not many, mind you) were applying the wrong set of rules to the narrative, basing them on the finale of ME3. For example, the fact that the Crucible is a galaxy-wide indoctrination device doesn't really have a lot of sense if we go with the information about the Catalyst and the Reapers that we were force-fed in the last few minutes of Mass Effect 3 - it does however have *a lot* of sense in *this* here narrative, with my take on the Reapers, their goals and motivations. This isn't a promise of handwaving - it's a statement to treat this story as a rising narrative, not a flat one - one where additional information is supplied at precise points in the storyline, selected to optimize both the emotional and "mystery" aspects of what's going on. You saying "I expect an explanation promptly" basically means that you're expecting an RPG rules book instead of a story - a codex entry, not a comic. And that's not exactly what I'm producing here.
"I'm not going to wait long for the author to give an excuse" - so, I'm guessing you're usually starting a new TV Show or a book by reading all the spoilers and everything Wikipedia has on the subject, then? Me, I'm not really a fan of reading the last page of a murder story just to know whodunnit. The little sentence I've just quoted shows that you are approaching this story with unreasonable expectations, having more to do with how I choose to present the events unfolding - and at what pace - rather than with the story itself. I cannot help you with that, sorry. I'm crafting this in a way that I find satisfying myself - and it seems that most of our readers are rather pleased with the achieved effect.
Your last paragraph has a major logical fallacy. When you start watching a new show or reading a new book, there is no canon established. The author sets canon as the story progresses. With Marauder Shields, you are basing it on what has already been previously established in the Mass Effect series. Just like as if you were writing a sequel to an original work, you don't have the luxury of saying "this and that is possible in this story" when previous canon states "um, no it isn't." If I were to read a sequel to an original work which immediately starts off with an element that is impossible—not questionable or unlikely, mind you—based on what was established in the previous work, I would put it aside. I have the same standard for "fan" work.
And do try not to immediately associate "reader" with "fan." I doubt that no one else has read the comic and had the same issues that I've had. I remember one article about your webcomic that mistook "page views" for "people who think it's a better ending"; the article was corrected by a commenter whose reaction, while overreacting a little, is quite understandable given the depressing journalistic incompetance I've seen regarding ME3.