@Angel Fear: I could summarize some of the basic points being made but if you're willing to slog through some YouTube videos there are those that address some of these points more elegantly than I could. The "understated nerd rage" and some of the Smudboy videos are some of the more famous examples where folks take the events of the series and analyze plot structure, story elements, shifts in the central conflict, etc.... You may have to ignore some unwarranted / inaccurate attacks or similar but there are some real nuggets to take away from these efforts. [IMHO ... YMMV]
To summarize [poorly]:
-- The central conflict for most of the series was basically "We must stop the Reapers from killing us all". The central conflict shifts in the last 10 minutes to something similar to "We must stop the cycle of organics creating AIs that inevitably rise up to kill their creators"
-- The genre conventions / internal lore is abandoned in places at the end to invent things like Synthesis [basically Green Space Magic] without much in the way of lore backing this up as being possible ; and explanation made so we understand what it does & why ; etc.
-- By Narrative Cohesiveness I'm referring to making sure that events that happen in the game are well explained and supported well by what comes prior in the game itself. While you can certainly forgive some instances of "that wasn't supported by lore or by what happened earlier but it was so dramatically cool I'm willing to overlook it" there's a lot of unanswered questions like why did the Reapers conduct such a passive war, why did they allow construction of the Crucible, if there was a controlling AI on the citadel why did the keepers need to "send the signal", etc. When you build up a lot of issues like this the story can unravel and you're left with a mess.
-- In terms of story conventions you can view ME1 as setting the initial premise / inciting incident(s) / explaining the rules / etc. It does a pretty good job of this. ME2's logical job would be to provide / continue the "Rising Action" part of the plot structure. This part of the plot consists of the hero fighting any obstacle(s) and conflict(s) in the way of reaching his goal. Most importantly the events [and solutions thereof] logically lead to the climax of the series. I would argue that, at best, ME2 is just an interesting set of stalling actions that do NOT contribute to the climax of the series. In ME3 they introduce a fix from on-high that is largely unrelated to anything we found in ME2 thus making ME2 a waste in terms of contributing to the overall arch of the story.
-- In ME3 because we stumbled onto the fix a lot of the sense of agency is lost because we don't even know what the thing does, how it does it, or even if we should really build it. As another poster put it recently the Protheans saved our butts in ME1, ME2 was a set of stalling tactics, and ME3 was an exercise in paint-by-numbers and hope for the best.
Honestly I'm sure there are a lot of other criticisms but this is what I can think of at 2 AM.
FYI: While I'm still disappointed in how the ME trilogy turned out I have recently found that I "miss" the universe that BW created. So while I cry & moan & b|t** about a lot of stuff I think BW was on the verge of creating something REALLY special -- possibly THE RPG series by which all other series in our generation would be measured by.