For instance, if Harbinger doens't blow Normandy up when Normandy is hovering right in front of it, it just makes me automatically give the screen the middle finger and thereafter laugh at trageties such as Anderson dying because that plothole just made the game a comedy and I cannot get immersed in the experience as it reminded me how cheap a fiction show it really is. The same goes with other factors such as characters, pacing tones, dialogues.
The Normandy evacuation scene is actually a great example of what I'm talking about. Even if you had a completely plausible in-universe explanation of how it could happen, the scene doesn't work at all. The tone of the beam run is one of total desperation; it's exactly the wrong time to introduce a sentimental 'last goodbye' sequence, particularly when we already had last goodbyes with our squadmates not an hour ago. The scene creates a tonal inconsistency for the sake of hitting character beats we've already hit. If you didn't have those tonal and story issues, I'm not so sure that people would have complained about the plot inconsistency so much. It would still be annoying, but probably more of a minor annoyance.
In ME, you can't even get past the fundamental backstory structure of the setting (of the Reaper cycle) without confronting how it's a really, really stupid way to go about any deliberate and systemic process. Whether preventing AI's or Dark Energy or Reproduction any other goal with an objective, measurable purpose, the Reaper cycle of crushing civilizations after they grow (rather than simply pre-empting them) is really, really stupid. About the only motivation in which killing everyone on a cycle like they do makes internal sense is if they do it for fun.
This is something I've always felt to be the case as well. It seems clear that the considerations driving how the idea of the harvest was constructed were entirely meta in character. The Reapers want to wipe out all life because that gives even the most murderously sociopathic of Shepards a reason to oppose them. They wait 50,000 years because if they didn't, the setting wouldn't be possible. The 50,000 year period also provides a context with which to introduce the familiar trope of the ancient advanced civilization that was wiped out mysteriously long ago (i.e. the Protheans). But I doubt that the cycle was designed with any particular view in mind as to what the Reaper goals would be, and how they would accomplish those goals.
That wasn't sudden. It was built up from Mass Effect 1.
You can have Shepard play devil's advocate in the first game, and point out to Tali the problems with the Quarian perspective while she is describing the Morning War. You can have Shepard point out that the Quarians started firing on the Geth for asking if they had souls. It was clear from the first game that the Quarians were the aggressor in the Morning War.
Then Mass Effect 2 introduced Legion, and had it explained that the Geth that followed Saren were a minority of 'heretics' who are opposed by Legion and the true Geth.
Long before ME3 released it had already been established that the Geth weren't villains.
I don't think we can completely say it was foreshadowed in ME1; we didn't know about the Heretic/'true Geth' divide, so for all we knew, all Geth were collaborating with the Reapers. This would make them villains: villains who'd been wronged by people who no longer exist, but villains nonetheless. It probably didn't help that Legion was introduced so late in ME2 (a major mistake IMO). Because of this late introduction, the transition from the ME1 characterization of the Geth to the ME2 characterization wasn't handled as smoothly as it could have been. As it is, Legion has to introduce an enormous amount of exposition in a limited amount of time; there's no way he can clear up all the little inconsistencies (i.e. if the Geth oppose the Reapers, what were they doing in ME1?, etc.) in that short span.
Don't get me wrong; Legion and the Geth are some of my favorite things about the whole series, but I do wish that some elements of this arc had been handled with more finesse.