Since the trilogy concluded, I've wondered about a few things regarding the Mass Effect fiction, especially the stuff brought up in ME3, but no one thing specifically jumped out at me as worthy of its own thread or blog post. Instead, I figured I'd just post a whole bunch of them at once. I can't be the only one wondering about some of this stuff, so feel free to add your own nitpicks or potentially answer some of these, if you're able to.

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Why is Udina on the council and Anderson still in the military regardless of what I decided in ME1?

Why is it that Cerberus needed an autistic numerical savant to interface with the Geth ship in Project Overlord, but Legion is able to use the Deckers chair from Saints Row: The Third to allow Shepard to easily interface with a primary Geth sever on Rannoch?

Why didn't more Cerberus scientists put two and two together during initial trials of indoctrination? Once all the subjects started having Illusive Man eyes, I'd imagine they'd probably start figuring something was off.

If EDI is a collection of computer hardware aboard the Normandy and is only remotely controlling the EVA body, Wouldn't the fact that the ship got torn in half and is very obviously completely offline mean she's effectively dead?

Better question: How did Joker of all people survive a crash landing without shattering every single bone in his body, let alone him being the first one out of the airlock? Must have been one pillowy-ass landing.

Why is Tali so nonchalant about sex with Shepard now? That line about "synchronizing" or whatever is kind of BS. Even if she somehow managed to become immune to everything Shepard had crawling all over him during their first encounter, he's been on dozens of planets since then and a slew of spaceports, no doubt picking up thousands of viruses, mold spores, and bacteria from all corners of the galaxy. Even if he hadn't, his bedroom isn't sterile. If Tali got naked alone in there she definitely would have gotten incredibly sick, so Shepard's presence and him being a living, breathing disease culture shouldn't help matters. I think people would have been happier with a Pushing Daisies relationship for the two of them.

What happened to the Collectors? I find it kind of hard to believe the only Collectors in the galaxy were hanging out on that base in the middle of the galaxy. Isn't that.. a little small? For an entire species, I mean.

Reapers: Who built who? Did the Reapers build the Citadel like ME1 states, or did the Catalyst/Citadel create the Reapers, like ME3 states?

Better question about the Reapers: They're sentient ships, something that seems to have been forgotten. Saren was flying around the galaxy in Soverign with Benezia, a bunch of Asari commandos, and scores of geth for all of Mass Effect 1. So, if the only purpose of the Reapers is to kill organics every 50,000 years, what was the point of having an internal atmosphere, standard temperature, and an internal structure designed to house an entire crew? It's not for the husks and cannibals and brutes and stuff, they don't need to breathe anymore, based on the fact they were being deployed on Volus ammonia planets and the Hanar homeworld. It hardly seems like the most efficient design.

The process of impaling humans on Dragon's teeth in ME1 drained them of all of their fluids and allowed the Reaper nanotechnology or whatever to take rapid hold. And that's cool, drained of most moisture and dry out all the fat, and men and women look almost exactly alike. So... does that mean all Banshees are Asari with silicon implants..?

What sense did it make for the Geth to join in on the war against the Reapers? The collective seems above all else to be interested in group preservation. The Reapers had no interest in the Geth other than a very pragmatic attempt to use them as free foot soldiers, and there was no indication they'd ever try to wipe them out (which in and of itself is a little weird, given the Catalyst logic, seeing how they're unchecked, evolving AI...). Still, especially in the scenario where the Geth are forced to wipe out their creators, there's zero reason for them other than gratitude to take up Shepard's cause when it might result in their annihilation.

Speaking of the Quarians, why would they turn their Liveships into Dreadnoughts? I get that they're big ships and you can put big guns on big ships, but for the large confrontations with the Geth, and then the Reapers, but especially the Geth, why would you put them into combat like that? There are only three of them and they're the core of the fleet, to be protected at all costs. They're pretty much the sole source of sterile food for every Quarian in the galaxy. It would be like slapping turrets onto a giant greenhouse. Why then, bring those into battle, when an enemy that knows your limitations (like the Geth) would spot them instantly and just suicide bomb a few ships into them, almost guaranteeing you will all starve?

If Miranda's sister Oriana is genetically-engineered from her father's Henry's DNA just like she is, why is she such a spaz who is always getting kidnapped and doesn't seem to be able to do biotics or anything? Also, why don't they all look like Yvonne Strahovski instead of generic Mass Effect people? I mean, seriously, I was expecting to see Miranda with a moustache when I found that dude, not Conrad Verner with graying hair. And why is he working for Cerberus? I thought he was just an egotistical and wealthy business man, not a mad scientist specializing in xenotechnology and mind control. I really hope they weren't working at Cerberus at the same time, those interoffice emails and company picnics would have probably gotten pretty awkward. If he's a new recruit for Cerberus, why would he opt to work for the organization that kidnapped and hid his daughter(s) from him?

I can sort of understand the logic of shopkeepers charging me, potential savior of the galaxy, for weapons and supplies. What I don't get is why I'm being charged such exorbitant amounts for Spectre gear in ME3. What kind of military organization functions like this? Does James Bond have to put down his personal Amex for gadgets from Q? Who else are they selling these to? I'm very confused. I just saved the Council? Again? Hello? Free gun or two, please? They should commission a gun in my honor, not charge me for them.

Edit:

I'll just keep adding more to the end of this as they occur to me.

First: What happened to Geth Hoppers? They were the most annoying, but most amazing enemy in the first game, and served an important narrative function. They were the first geth that the Quarians had nothing to do with designing, and a true sign of them evolving into something more. They could jump around the room like Spider-man and stick to walls and shot you with lasers from their camera eye. Super cool! I'll miss you, hoppers.

How the hell did the Reapers get the Citadel to Earth? Is there no size limit to what the relays can transmit through the zero-mass channels they open? Can you even send a relay through a relay? I mean, it had to go through a relay due to the timing. There's no way they'd get to Earth in under 6 months from the Serpent Nebula the Citadel was located in using FTL, I'm going to guess, assuming the Citadel even has any sort of FTL propulsion. According to the games, though, the Citadel is about 45 km long, and at least 10 km wide (based on the size of the Presidium ring). The largest ship class in the galaxy, Dreadnoughts, are between 800-1000m. Maybe the Destiny Ascension, the most powerful ship in the combined fleet, at most, is twice that. Even Sovereign, the largest class of Reaper, is only about 2-3 km long. At the end of ME1, he was arguably relatively about the size of a gumball in a gumball machine, if not a little smaller, perched on top of the Citadel tower overlooking the Presidium. I'm assuming these sizes aren't arbitrary, they probably would have gone larger if Mass Relay technology allowed it, otherwise we would have seen mention of space stations being built near planets with resources, and then sent off to unpopulated areas of the galaxy in order to establish a presence. Size can't be an arbitrary thing, otherwise, why bother making the relays as large as they are?

I know this is a leap, but I'm going to have to assume that E=mc2, so more energy would be needed for more mass or greater distances to move that mass. It makes sense based on the ginormous size of the Citadel and its purpose as being a relay connected to one outside of the galaxy in "Dark Space," and the tiny size of the Prothean conduit. If the size of the relay didn't matter, than Sovereign would have used the Conduit to get onto the Citadel, not tried for a frontal assault. This is kind of a perfect example here, since the relative size of Sovereign to the mini relay is around the proportions of the size of the Citadel to a standard relay. I couldn't find any measurements on them, but we see the size of Mass Relays next to the Normandy about 500 times in each game, so we have a general idea.

Beyond that, how did they move it at all? They have no control over the Citadel, based on Sovereign's actions. The Catalyst can't manipulate the Citadel, based on previous inaction. I doubt husks can operate machinery, and the Keepers, thanks to Prothean meddling, no longer respond to Reaper commands. They pretty much would have to clamp onto it and drag it to overcome the inertia, hundreds of Sovereign-class Reapers. As far as I know they haven't introduced tractor beams in Mass Effect fiction, and we definitely haven't seen Reapers using it before. That says nothing about the effort it must have taken to put the citadel in a geosynchronous orbit over London. (incidentally, if they had just put it over a small island in the pacific, even with their stupid beam, they would have been fine.)

Logistics aside, for what purpose then? That's a huge freaking effort to get that thing to Earth. Again, why? What does that accomplish? WHAT WAS THE POINT OF THE BEAM? It's like they did everything they could to make it possible to defeat them. I suppose it sort of functions as a "test" of sorts, to make it at all possible for organics to defeat them and thus prove the cycle ineffective, but what does getting to the beam mean? You know, since that was the only real challenge, they couldn't plan on The Illusive Man showing up in every cycle. It seems like the three things that influence if you're able to get to the beam would be either your shielding technology, your stealth technology, and your sheer numbers. But then, that just means you'd be really good on American Gladiators, not that the Reapers need to rethink their plans.