This thread is gold. I love this franchise, I really do, but sometimes it drives me insane. In addition to what has been said...
Nirali Bhatia: They tell Shepard that her body is totally and absolutely required to develop countermeasures against geth weapons and if you decide to return the body to her husband, then in ME2 you can hear about the Alliance being unable to match geth technology. Despite the fact Eden Prime had dead geth and their weapons scattered all over the place.
Horizon: Why does Kaidan, a biotic, try to shoot the seeker swarm instead of using his biotics? We already know he has quite a self-preservation instinct. Vyrnnus could tell a story or two about that. Oops, wait. So why would a biotic ever shoot a swarm of insects? Actually, why would anyone? The only reason I can think of is a/ trying to scare them off (But still, really?), b/ trying to draw their attention while the colonists escape. (Which would have zero effect anyway as the colonists just stand there like a bunch of dodos and watch, despite being told to run.)
The Virmire Survivor telling you that they came to Horizon in order to investigate Cerberus presence, but then they leave without interrogating Shepard.
The Alliance sending one person to deal with this problem. Actually, the Alliance basically doing nothing besides that, despite hundreds of people mysteriously disappearing.
Anderson not telling the VS that Shepard is alive. I understand he couldn't tell Shepard anything, but why keep the VS in the dark about it?
While I understand and approve of VS's reasons for not joining Shepard, the Horizon dialogue is just so badly written. Especially because Shepard barely explains anything, no matter your dialogue choices, and there's very little dialogue to be had in general.
Grunt: Shepard releasing Grunt from the tank without somebody backing them up.
ME2 and ME3 in general: Exposed skin and eyes in space. Plus, catsuits instead of armour.
Chestplates for ladies made of hard material with boobs moulded into them. What?
Mars: Watching the sexbot escape on the shuttle was extremely jarring for me as somebody playing a Soldier Shep that has grenades but does not even try to throw one into the vehicle despite the door being wide open.
Why does Shepard, an experienced soldier (My main is a Mindoir suvivor and Akuze survivor, on the top of that.), the N7, the Spectre, the hero of the Citadel, the destroyer of worlds, somebody who can fearlessly punch a yahg in the face, all freeze up when the sexbot attacks the Virmire Survivor? Like, the sexbot has enough time to call TIM and get instructions before it actually does anything! That's a lot of time. Shepard's natural reaction should be to goddamn gun it down and if it were too dangerous for the VS, we've just got a shiny new omni-weapon. Having Shepard stand there and watch like an idiot as the VS gets their ass handed to them makes zero sense and it reeks of an attempt to forcefully throw in some drama.
Speaking of which, the VS is more than capable to handle themselves. Hell, both Ash and Kaidan have had synthetics for breakfast in large numbers since the day one. Now they can't take out one half-fried robot? Plus, Kaidan is a Sentinel. That means that he can either overload it or freaking punch it from distance if he so wishes (and we even see him do such things in the Citadel DLC if romanced, which makes the Mars scene even more ridiculous).
Shepard being all drama queen after this happens and being uncooperative. "Kaidan got hurt. And what about Kaidan? I'm gonna check on Kaidan. *grumpy face*" I did romance him but, hell, stop it. I get it, you give a damn. But thousands of people are dying, pull yourself together, Shepard. I like that they tried to give Shepard more emotions and I do like some parts of it (Like Shepard standing over him in the medbay, looking shocked and distressed. That was enough to convey Shepard was worried about him, imho.), but turning them into a sulking love-struck teenager is too much. (I do think it got better from the end of the Mars mission on, though. At least I don't remember other instances of my Shepard going "KaidanKAIDANkaidanKaIDaNn").
Utukku: If you decide to save the queen, you never actually see her escaping or escape.
Why are we leaving Grunt to hold the rachni off all by himself? We've just shot through a whole army of those things. Plus, four people are more than one. PLUS, don't we need to make sure that the queen gets out all right since we've sacrificed people to allow her escape?
How does the queen get off the planet? I doubt the Kodiak took her.
Quarians: You know what the intergalactic war needed? More war!
Trying to shoot down a dreadnought with one of their most important representatives and one of the most important galaxy's representatives that is trying to ensure the survival of the whole galaxy aboard because it just couldn't wait a few minutes, especially after Tali and Shepard went through the pain to make sure to disable the dreadnought.
Krogan: Sorry, but being able to have 1000 babies per female a year is bull. Maybe insects can do that. I mean, how is that even supposed happen? Do they have several babies every few weeks or something? Or do they just pop out a few hundred kids now and then? Or do they simply produce a few babies a day? Damn, being a krogan woman must suck. Also, there's a reason animals have only so many babies. No mother and no parents are ever going to be able to feed and take care of 1000 children. Even less so if they're going to produce 1000 more every year. (Always having 1000 is an extreme scenario, but that's how it's presented to us in the game.) Most of those children would simply die of neglect, unless krogan babies are extremely self-sufficient since very young age. And if they were to survive, their planet would have got depleted of resources a long time ago and there would perhaps be very few surviving krogan to speak of. They wouldn't have even been able to get to the point where the salarians "uplifted" them. Look at what happened to the drell. I call bull****.
Leviathan: Once upon a time, there was this omnipotent race that realised that the synthetics will always turn against the organics (Who cares that Shepard can prove that to be total crap.) and with this knowledge, what do they do? They create a synthetic to handle the problem and they do not monitor its activities. Their explanation? "Well, crap, we thought we were too badass and cool so that the rule didn't apply to us."
So, the reason the harvest and the cycles and the Reapers exist, as explained by the Leviathan, is basically, "Oops, we f'd up. Our antivirus went kinda bonkers there. Sorry, not sorry, LMAO." Legit.
Leviathan sitting at the bottom of the ocean for devil knows how many cycles and doing absolutely nothing to at least try getting rid of the Reapers during the 50k year breaks they have between each harvest. Talk about being passive.
I really like the Leviathan DLC, but come on. Desperate attempt to justify ME3's completely messed up ending providing absolutely laughable explanation for the existence of the star brat.
The Reapers: THERE IS NO WAR. THERE IS ONLY HARVEST. *proceed to fry everything and everyone to dust instead of, you know, actually harvesting*
"We can't beat the Reapers conventionally." I don't know how many times Hackett shoves that down out throat. Then Shepard proceeds to destroy a few Reapers, then you hear about some of the capital ships being taken down on the news (Like on Feros! The Feros colonists actually took down a Reaper capital ship. I don't know how but go, Feros.), then we enter the Reaper controlled space to take back Earth and we see a Reaper capital ship being shot apart right in front of our very eyes. "Can't beat the Reapers conventionally" my foot. I'm not saying that means victory for the galaxy; I'm just saying that the Reapers can be and are being conventionally fought and destroyed.
London: Humans engaging ravagers and other Reaper zombies from up close. Have they not studied and analysed how the individual Reaper monster types fight in order to develop strategies against them? Pretty sure those guns can shoot farther than 10 metres, too, so no need to get into immediate distance.
The Harbinger patiently waiting for Shepard to tell their love interest that they love them before evacuating them. I guess the Reapers have a thing for drama. Maybe that's the whole point of the harvest. They like to see some blood and tears. Would still make more sense than the original ending. Perhaps the harvest is just a major troll attempt to get a rise out of the organics.
Going to the beam on foot when we are shown that we could've used the Normandy.
Hackett not sending people in after the Citadel's arms open and relying on Shepard to do it on their own. We don't know what's in there. There could be a Reaper army ready to attack, for all we know. What kind of admiral is Hackett? All we get to hear from him at that point is, "Oh, ****, she/he did it!" and "OMG, SHEPARD, IT'S NOT DOING ANYTHING!"
The ME3's ending: Everything. I have no words to even begin describing the complete and utter pile of bull that is the ME3's ending.
EDIT: Well, I went a little overboard...