Here's a list of questions I expect the Extended Cut DLC to answer. A lot of these questions were raised in the last hour of Mass Effect 3 and simply didn't need to be raised in the first place. Some of the questions are so mind bogglingly complex and absurd I don't think anyone could possibly try to answer them. If Bioware were to rewrite the ending from the ground up, 80% of these questions would magically disappear and would not need to be answered.
Anyway, just to give you an idea of how horrendously confused I am, here goes.
How does synthesis work? How can a wave of light transform DNA? I know for a fact that electromagnetic radiation tends to damage or kill living cells. It definitely cannot repair them or fuse them together with a synthetic material. To do so would also kill the cell. I also know that green light is in the middle of the visible electromagnetic spectrum. The photons associated with green light have lower energy than blue photons, as the frequency of blue light is higher than green light. By Planck's law, the energy of a photon is E=hf where f is the frequency and h is a positive constant called Planck's constant. If anything, blue light has a higher chance of causing any molecular change within DNA because blue light may contain photons in the UV frequency spectrum, and UV photons can be ionising. Green photons are non-ionising. When we shine green light on our skin, nothing happens. When we shine UV light on our skin, we get a tan, because the photons have sufficient energy to ionise the atoms and molecules within our cells.
Surely, then, the synthesis option should use blue light, or UV light or any radiation of higher frequency than this, in order to facilitate a molecular change of any kind, and not green light? We also know that visible light is easily absorbed by solid matter such as rocks present on the Earth. What about the people on the other side of the Earth? Did they get hit by the synthesis electromagnetic pulse? is that even possible? Surely the eloectromagnetic pulse would only be able to coat a maximum surface area of one semi-sphere, and hence not cause synthesis within the entire human population? We know this because the Sun is a point source of visible light and this light can only cover roughly half of Earth's surface area at any one time, because the light that hits the Earth is quickly absorbed by its surface - hence we get the day-night cycle.
So, will EDI now be able to have children now? Did the synthesis process give her internal organs to make her capable of reproduction? Did the same thing happen with the Geth? What exactly happened to the Reapers? Weren't they already cybernetic, a mix of organic and synthetics? How did that even work anyway? Weren't the Reapers originally just a race of machines as established in Mass Effect 1, a race of true artificial intelligences, hence not organic in any way? Why did this change in Mass Effect 2?
How does controlling the Reapers work? How can Shepard control the Reapers if he's dead? How can Shepard give orders to the Reapers? How can the Reapers possibly be controlled if they themselves are "true artificial intelligences" and thus capable of free will?
Why did the destroy ending involve shooting a glass tube? How does shooting a glass tube, or part of a machine, activate the machine and not break it? Why did Shepard walk towards the explosion? Why did Shepard or I have any reason to believe shooting the glass tube would work?
Why is Joker running away from Earth? How did he get to the mass relay in time before it exploded and sent the energy to the other relays? The energy blast from the relay, when viewed from the galaxy map perspective, is clearly moving at roughly 80,000 light years a second - how is Joker possibly able to outrun this energy blast? Why does the energy blast damage the Normandy's engines when in the scene before on Earth, the blast did not damage the forces on the ground? Did the relay explosion damage the ships in orbit above Earth, and cause those ships to crash land on Earth? How could they have managed a safe landing? Surely if the crews of the victory fleet either lost control of their engines, or had their engines destroyed, that would have made entering the Earth's atmosphere incredibly dangerous or perhaps fatal? Did the relay explosion cause any other damage to the victory fleet ships, if so how bad was it? Were there any hull breaches? Was anyone sucked into the vacuum of space? Did anyone need to be resurrected by another Lazarus project? If the relay explosion took out the Normandy's engines, did it take out the element zero drive core as well? If so, did the Normandy lose artificial gravity? If yes, then does that mean all the ships in the victory fleet lost artificial gravity also? What would be the consequences of that and how would the fleets manage a zero G environment as they plummet towards Earth? Do they still have kinetic barriers? Will they be able to enter Earth's atmosphere without burning up?
How did every member of my squad get back onto the Normandy? Why did they get back onto the Normandy? When did they get back onto the Normandy? Where did they get back onto the Normandy?
How did the Normandy crash onto a perfect jungle like planet? Aren't those the rarest planets one can possibly hope to find in the galaxy? How could they have possibly been that lucky, particularly if their engines were destroyed, and Joker had absolutely no control over where and how they were going to land? How did Joker know the air was breathable? What kind of food is present on the planet, and how will the either the L amino or D amino crew members avoid starving to death? Is the food toxic like on Jacob's loyalty mission in Mass Effect 2? How are they going to survive?
What does Liara think of all this? Does she know that Shepard is dead? Is she not worried that he might be? Does she not miss her lover? Is she not upset she won't be having any blue children with him?
What does Garrus think of all this? What does Tali think? What does Javik think? What does EDI think? What are the thoughts of all these people on what happened:
Samara?
Zaeed?
Miranda?
Jack?
Steve Cortez?
James Vega?
Ashley?
Grunt?
Admiral Raan?
Primarch Victus?
Wrex?
Bakara?
Kasumi?
Admiral Hackett?
Daro Xen?
Jacob?
How did the Citadel move to Earth? How is it able to move? Does it have thrusters? Where are they and how do they work? How did the Reapers control it? How did the Reapers take control of the Citadel? Did they kill the council? Did everyone on the Citadel die? What happened to Commander Bailey, and all the other people on the Citadel?
Who is the Catalyst? How do we know that what it is saying is reliable or even true? Why does it look like the child from Shepard's dreams, when in real life that child is dead? Why does the Catalyst or Shepard not mention the alliance between the Quarians and the Geth as a valid counter argument to the Catalysts motives that must be addressed? How can the Catalyst control the Reapers if the Reapers are supposed to have free will? How are the Reapers functioning as organic civilisation hive minds if they are being controlled by the Catalyst? Why can't the Catalyst offer some valid proof that it does indeed have control over the Reapers? If the Catalyst has been present on the Citadel all along, and it is the force behind the Reapers, why didn't the Catalyst take control of the Citadel prior to the events of Mass Effect 1? If it controls the Reapers, it controlled Sovereign in Mass Effect 1. Why then, did it need to indoctrinate Saren in order to gain control of the Citadel if the Catalyst was present on the Citadel all along?
Okay, here's the big one!
In Mass Effect 1 it is established that the Reapers built the Citadel. How did they build the Citadel if the Citadel is the Catalyst, and the Catalyst is the one who built the Reapers?
(This is the biggest reason why the Catalyst must be removed. You cannot hope to logically explain this. It is impossible).
Who created the Catalyst? Is the Catalyst an individual or a collective? Why does it refer to itself as an individual and then as a collective? Is there more than one Catalyst? Is the Catalyst a Reaper? Why does the Catalyst not have any resemblence to a Reaper, if it was the one who created them? Why does it look like a human child, when it has clearly been in existence for millions of years before humanity even evolved? The Geth bear a resemblence to the Quarians, reminiscent of the idea of the Christian God creating man in his own image. Why did the Catalyst decide to design the Reapers to look the way they do? Why did he give them the ability to indoctrinate, torture and mutilate organics? Isn't that an extremely cruel way of controlling the population of sentient races? If the problem is synthetic life, than why not use some elaborate electromagnetic pulse device that destroys all electronics to send the races of the galaxy back to their respective stone ages? Wouldn't that solve the problem, without having to kill anyone? If the Reapers are trying to convert organics into Reapers, then why are they indiscriminately vapourising them with lasers? Wouldn't it be better to take out just the military forces first then harvest the rest?
How can a Reaper be an organic civilisation hivemind if all the members of that organic civilisation are rendered brain dead during the Reaper transformation process? Why are they not taking the brains of their victims, where all the intelligence is stored, and trying to preserve them? Surely they would want to keep the brains intact at the very least? Where does the Reaper's intelligence come from then? Why does the Reaper need dead organic tissue anyway? Wouldn't that cause the Reaper to be damaged by harmful electromagnetic radiation in space, exposure to space vacuum and near 0K temperatures? How can a Reaper be immortal if it is made up of organic material that withers and dies as time progresses?
What is a Thanix missile? What does it do that makes it more effective than other weapons for killing Reapers? Why wasn't the targeting laser from Rannoch used at all? Why didn't we try using the Cain a bit more if it was able to destroy a Reaper Destroyer in one hit? Why didn't Shepard tell anyone how to kill Reaper Destroyers in this manner? Why didn't any member of Shepard's crew, such as EDI and Liara, tell anyone how to destroy Reapers, or provide any valid assistance?
What role did the members of Shepard's squad play in the final battle? Was there any point in bringing them?
What role did the Geth play in the final battle? Was there any point in giving them true sentience and allying them with the Quarians?
What role did the Quarians play in the final battle? Was there any point in giving them back Rannoch and allying them with the Geth?
What role did the Turians play in the final battle? Was there any point in saving Palaven?
What role did the Krogan play in the final battle? Was there any point in curing the Genophage?
What role did the Asari play in the final battle? Was there any point in trying to save Thessia?
What role did the Terminus fleet play in the final battle? Was there any point in recruiting the merc groups with Aria T'Loak?
What role did all those scientists on the Crucible play? Was there any point in assigning them to the project?
What role did the Rachni play in the final battle? Was there any point in showing mercy in Mass Effect 1 saving them from extinction?
What role did Javik play in the final battle? Was there any point in paying £10 to unlock him?
What role did the Salarians play in the final battle? Was there any point in helping Kirrahe survive Virmire?
What role did the colony at Zhu's Hope play? They were a war asset right? Was there any point in saving the colonists in Mass Effect 1?
And finally, was there any point in ANYTHING that happened in Mass Effect 1, Mass Effect 2, or the events of Mass Effect 3?