Things that don't make sense (v2)

Boob-shaped armor.

In ME2, during the scene where
 EDI states that she has purged all life-forms on the ship. But (fortunately) my fish and hamster are just peachy.

I sent Jacob to the vent during my first run of the SM; he volunteered so i went "ok sure, go right ahead" and true to the trope of the black man being the first one to die, he bit the bullet.

Either that, or Joker made an emergency run to the pet store before Shepard got back and hoped s/he wouldn't notice.

How does Anderson plan to go and help with the fight from his dropoff point in Vancouver? You just see two shuttles get crashed and there are 3 visible Reapers in the vicinity and Anderson is standing alone in some crashed docks.

Another thing is THE PLOT OF ME3. Hear me out. Your premise is to save Earth from the Reapers and then the galaxy, but we don't know how becuase all we have to go on is that Shepard leaves Earth to get "every fleet" he can from the council races to help Earth, but the second we get further away from Earth we can tell there are Reapers everywhere in the galaxy already but we still keep this "Save Earth" mantra even though "saving Earth =/= saving the Galaxy" so the plot is on shaky ground as to what exactly we're even doing, but we go to Mars as per Hackett's orders and being with the Alliance to find the plans for the Crucible which can defeat Reapers. Gotcha, sounds completely implausible to me or even that Protheans all of a sudden "came close to defeating the Reapers" but let's go with it. Great, let's pour all our resources into finding a way to build this machine... oh, I forgot, we still have to save Earth by recruiting aliens who are already busy with THEIR homeworlds because nonsense. But then you get to the Cerberus HQ mission and finally find Mr. Prothean VI who reveals to you that to finish the Crucible you need the Citadel... which has been moved to Earth... OOoooohh!! NOW IT MAKES SENSE..... except, it doesn't because it only makes the plot work retroactively. We never knew Earth was an important scene when it comes to "STOPPING REAPERS = SAVING THE GALAXY" until we learned the catalyst for using the machine to stop all Reapers is literally orbiting Earth.

The plot is a complete mess. You can justify lending forces from aliens for Earth while their homeworlds burn as much as you want but I'm not buying it. I think helping the Krogan and Turian relations or Geth/Quarians as a means of peacekeeping to avoid infighting when the galaxy is in dire need of everyone's strengths focused on killing Reapers makes total sense, but obviously not as a motivator for Shepard but the idea they came up with instead of rallying people for Earth before it makes any sense to do so outside of humanitarian ego, doesn't work either, and to think this plot is the result of extensive peer-reviewing and thinking about how one-sided this "SAVE EARTH" plot probably was in the first draft scares me.

One thing that could have made Cerberus a lot more relevant (beyond "evul") was if the necessary info to defeat the Reapers was on the Collector Base and we had to get it back from TIM. There's also a reference in LotSB where Liara mentions things the Yahg broker had found or was investigation about the Reapers. Having that info be relevant (and a reason for TIM to attack her) would have been nice as well.

There's a couple of problems with how Ceberus are depicted in ME3.

They have their husk-clone army amassed in only 6 months with or without the Collector base (it's completely irrelevant) so why did they need Shepard in ME2 if they are this efficient?

They preach about controlling Reapers and that is fine IMO but it's never convincingly alluded to that they're getting anywhere with it, and when the game tries to do so it's via rambling where TIM just vaguely talks about how successful Sanctuary was.

There's no real conflict of ideology between TIM and Shepard's "I'm right!" "No you're not!" conversations. It's one-sided because neither part elaborates on why they picked their stance and Shepard defaults to moronically talking about "destroying" Reapers. Firstly, we still don't know anything about effectively "destroying" Reapers for the majority of ME3 so Shepard's arguments are blind faith -- it's like hearing someone preach about anti-Trump and then when asked they don't even know his policies. Secondly, TIM and Cerberus is bluffing. They hint they're in it for controlling Reapers and go out of their way to convey this idea to Shepard but they never explain what exactly they're doing or how plausible it is. There is ZERO reason for TIM to even bother communicating with Shepard if he's not even trying to persuade him to either lay off or to join him.

The narrative can't decide whether Cerberus's role was just indoctrination or the plot of "control" held any water. It constantly goes back and forth between the intrigue of TIM being on about something to the other characters bluntly claiming he's just indoctrinated and in the end despite of getting the option to control Shepard's "So... the Illusive Man was right after all" doesn't even fit because we were never even second guessing ourselves or contemplating TIM's philosophy, and TIM never led us on about how he needed The Crucible specifically, so narratively it all feels like a giant waste of plot-developments that don't go anywhere.

To be fair, even if that would have worked, there would still be indoctrination to worry about. There was a large influx of refugees not to mention officials and other personnel with higher access that might have been indoctrinated like the Hanar agent in the Embassy. I think he was indoctrinated but I may be misremembering. The Reapers also had agents previously while in dark space so given that, there might already have been indoctrinated agents just biding their time at the Citadel until the right time during the invasion.

Anderson is clear that he feels that the people who remain stuck need someone to help them out.  It's not that he thought he could take on the Reapers himself.  It's that he thought he could save a lot of lives by taking command.  At least, this was super clear to me. 

It's a bug. I've never encountered that on that UNC mission.

Are you sure it's not the Alliance marines saying that stuff?  I'd have to replay that section but it seems more likely they're saying it than the rachni.