Okay... So I took a look at the first five chapters of this thing. Here are my impressions:
Well, the ICness of the characters tends to vary a bit. Miranda and Jacob were fairly OOC when they were first introduced (Miranda doesn't really harp on her 'second in command' status that much in the games, and Jacob isn't really the kind to be confrontational), and some other lines make no sense (Garrus and Mordin have a couple lines that don't agree with their characterizations.) But on the other hand, this is the most IC I've ever seen the Illusive Man in badfic, and the writer has Mordin's speech patterns down pat. So it's not totally in character all the time, but it's not the most OOC I've ever seen people get in this continuum.
I question the logic of a second omni-tool manifesting on someone's wrist, though. That isn't plausible, since omni-tools need a free hand to manipulate, and I'm pretty sure that the omni-tool also has to have something physical there, I don't remember what. It's not just a holographic interface, so... I'd chalk that bit up to Rule of Cool abuse, since it's there to allow Shepard a second omni-blade (which will be a canon weapon come ME3, so...). That bit doesn't work.
I'd also question the Normandy's ability to repel a Yamato cannon. If you upgraded the Normandy's armor and shields in-game (which I'm assuming this fic did because they make mention of some of the other ME2 ship upgrades), it's true that you can throw a very high-powered particle beam at it and still be safe. At the same time, though, the Normandy is only a frigate, and it was designed for stealth and excellent maneuverability, not for direct dogfighting. As I don't know how Starcraft tech goes, I'd have to know how a Yamato cannon actually works in order to accurately assess how easily the Normandy could withstand it. It is feasable for the Thanix Cannon to tear right through an enemy ship, though, as that particular cannon manages to take down a Collector cruiser in two shots in-canon. Seeing as how the Collector cruiser in question was a ship that was both larger than the Normandy and had superior technology, it's not too much of a stretch to assume that it could do some serious damage to ships of another continuum.
I'm not totally sure about how fast the Normandy takes down all the ships, though. Even for the Normandy, it looks like they take down a huge amount of ships in a ludicrously small amount of time. That might be a function of the prose itself, though, because that bit was very rushed.
There's a big issue you probably wouldn't think of that came to my mind while reading this, though. See, in ME canon, not all the aliens speak English. This is handwaved by the fact that these little things called "translators" exist that allow you to understand any alien language since they translate it for you. Crossovers tackle translators in different ways, but I think the most accurate depiction is to not have 'em if the other continuum doesn't have it. Again, seeing as how I don't know Starcraft all that well, I'd have to know for certain if the Starcraft continuum has translators. If it does, then I can possibly see why the aliens would be instantly understood. If not, that could possibly be a pretty big charge.
Hm... I know that the biotic barrier that Jack summons can block smaller objects from entering. But if said object is travelling at a high velocity, that makes me less sure because the biotic barrier they're talking about can't block mass accelerator rounds from either side, in both gameplay and cutscenes. Thus, I think it would be too much of a stretch to assume that Starcraft bullets can just bounce off the thing, so that bit at least is fairly implausible.
I know that Grunt would DEFINITELY be able to charge guys while taking a ton of punishment, but I don't think people would fail to notice him charging, given that krogan are huge in comparison to humans and that the aliens are probably stealing all the attention in this situation.
The whole bit about the ME-verse technology being based on Xel'Naga technology is actually really canon breaking for the ME-continuum, though. The thing is this: the Protheans inherited the mass relays, rather than making them. So did the species before the Protheans, and the guys before them, and vice versa. See, the technology of the ME universe is based on the technology of the Reapers that go in and destroy all organic life every 50,000 years, and it's been like that basically since the beginning of the universe. It plays into their Xanatos Gambit in rather large ways, which I won't go into here. The fact that all species are essentially unwittingly playing into the Reapers' plans by developing a technology along their path is thus a piece of the Reapers that plays as a pretty big plot point throughout the first Mass Effect. As Sovereign says in the first game, "We impose order on the chaos of organic evolution. You exist because we allow it, and you will end because we demand it." Thus, having ME-tech be suddenly based on Xel'Naga technology creates a massive plot canyon in the ME continuum. That is definitely implausible, and if this were ever to be sporked, then this would constitute a canon break in the ME continuum. I'm sure it would also create a canon break in the Starcraft continuum as well, given the nature of Prothean technology as I've explained above.
Reaper indoctrination not working in the Starcraft continuum is also very implausible. If the experiences we've had with indoctrination throughout the entire ME franchise say anything right now, nobody can escape indoctrination, especially since you don't know that you're being indoctrinated when you get indoctrinated.
So overall, my impression is that this fic is pretty canon-breaking for the ME continuum, but not in the way you'd expect. It's possible for the Normandy to do some of the things it does in-fic, but my bigger concern is in the stuff that attempts to bring the Starcraft and ME universes together, because it makes no sense at all and breaks canon for both continua. Honestly, part of me is wondering if this author ever played the first game, so yeah.
I'll have to look through the rest of this thing at a later time, but for now, those are my impressions.