Mass Effect 3, a game I still adore, made two critical narrative errors as far as I'm concerned that seriously diminished the previous exposition and intrigue.
Strike one was the Geth, and the choice to take them on a Pinocchio journey. The Geth were fascinating precisely because they were an intelligence that was totally alien in function and form of consciousness. Mass Effect 2 in particular explores this in an interesting way, with Legion challenging Shepard on a perception of consciousness and identity, the importance of not projecting a bias formed from the standard biological evolution of consciousness on the unique Geth experience, and the inherent dissonance between biological and machine intelligence and challenges of forming a future together. The Geth are pursuing a unique consciousness singularity, as a sense of purpose, in a way that biological organisms cannot. Mass Effect 3 completely uproots this narrative, and for all AI too including EDI, by transitioning the theme of consciousness to rigid biological constraints and forcing the Geth to pursue a sense of identity identical to our own. It completely abandons the uniquely alien yet totally plausible intrigue of their form of conscious for a dumb, whimsical, and overly romanticised idea of conscious limited entirely by our own existence. That the Geth's "solution" to their form is to just become exactly like us is an awful, uninspired, and completely vapid erosion of the great framework established before.
Strike two is the Reapers, because BioWare clearly had no fucking idea what to do with them. I don't subscribe to the notion that the Reapers need to be magical, but the way they're presented in Mass Effect 1 and 2 is in deep contrast to how they're resolved in Mass Effect 3. They begin as an omnipotent, powerful, and intimidating species that for all intents and purposes can be assumed to be an apex species (maybe the very first apex species) that views other living creatures like ants (a very real philosophical concept in AI theory) to be consumed for energy and resources, nothing more. By the time Mass Effect 3 is coming to its conclusion they're no longer an intimidating threat, but a runaway AI process aimed at preserving organic material that doesn't actually mean any harm at all. This idea is fine on paper, and the Leviathan DLC adds substance; a plot involving a runaway AI coming to unintended unethical conclusions based on prerequisite functions and goals set by its creators is not an original idea, but it's tried and true and again a theory in AI. But Mass Effect never, ever, not once implies, hints at, or presents the Reapers as anything less than totally conscious, deliberate, methodical, and overly intimidating and ruthless with a fully formed perception of organics. That being organics are disposable fuel and nothing more. It's the worst of twists because it's not reasonable or believable, has no substance given what came before, and seems to only exist to reframe the Reapers in a way that surprises the player and challenges them to think. The problem here being good stories need substance to pull that off, they need plausibility and logic for the twist to be believable, and with Mass Effect 3 it was like they just inserted a random idea for the Reapers right at the end that it's total contest with everything that came before.
So yeah. I know others will be a lot pickier and put scrutiny on many more narrative beats within the trilogy; characters, arcs, Shepard, etc. But those are the two that stand out and bug me the most, because they're the ones that left me very unsatisfied and can't readily be "fixed". They're highly indicative of writers who, for some reason, decided in the very last chapter that narrative threads would be about something entirely different from what they started, at the cost of the most intriguing and fascinating science fiction ideas.