I liked your ideas for a sequel, although my ideas vary from yours a bit.
First of all I cannot share your disdain for Andromeda. Obviously it struggled due to changing horses in the middle of the stream, being over-hyped, and being released before it was fully ready. Nevertheless, it is an entertaining game with interesting storylines both in regards to our continuing adventures in the Andromeda galaxy as well as implications for events in the Milky Way. With a good polish and a few fixes it would no doubt be an excellent game. As it is, on your grading scale it would probably rate in as a B or B-.
However, the most important thing is that its existence provides us the opportunity to create at least three excellent Mass Effect games, or even series.
First of all, in the Milky Way there is the opportunity to explore what happens if Shepard defies Catalyst. This is the ME3 ending where the Reapers win. However, we just found out that the true leader of the Reapers is Catalyst, and Catalyst is the Citadel. Since we just strapped The Crucible to the Citadel, and if all else fails, which it just did, The Crucible is a big freaking bomb, Shepherd would obviously call for the Allied fleets to blow it and take out the Reapers’ leader.
This is a game where the more War resources gathered and the higher your Galactic Readiness before the drop on Earth would make a significant difference. You are fighting a war that you have lost the ability to win. What you are attempting to determine is the terms of your failure. With a high enough military resources score and Galactic Readiness score you would potentially be able to have the Normandy recover Shepherd while detonating The Crucible, and possibly destroy Harbinger and a number of other Reaper dreadnoughts in the blast.
From here on out it is all about salvaging what we can from the wreckage. Obviously many of the campaign or multiplayer missions would revolve around rescue operations or last stands covering evacuation vessels. The Grand Alliance is trying to salvage in any way possible as much of its peoples as it can. Part of the story will therefore be determining how they're going to attempt to do this. In addition there will obviously be resource gathering, scouting, and surgical strike missions, possibly with a few other things thrown in.
An interesting twist would be playing some of the missions, especially suicide missions, as some of the characters we’ve met/heard of. For instance, playing as Sidonis as he seeks redemption.
The more troops you have left at the end of ME3 the more you have to start with in this game. While there would undoubtedly be some more resources to gather, the majority would be what you had retained from ME3. This would make a multiplayer system to increase Galactic Readiness incredibly valuable, as a high Galactic Readiness before each mission in the main campaign would allow you higher success rates and more surviving War Assets after each mission, making your future successes and survival a little bit longer and more likely. An interesting strategic twist would be to allow you to make use of all the teams that you have uploaded to War Assets when doing multiplayer. This would allow you to use advanced characters who would make your mission success significantly more probable. However, as these are liable to be suicide missions you would then sacrifice that character from that team and no longer be able to use it for further multiplayer battles, as well as taking a slight hit to your War Assets for this playthrough.
Obviously the Galaxy is doomed and most of the people there are going to die. However, we do have a number of tools to help some survive. First of all we have the arks. If you read the benefactor conspiracy theories you'll get a decent list of all the people who are potentially building private arks. In addition Liara almost certainly has full schematics to create arks, as do, most likely, a number of other intelligence organizations that Hackett has access to. This is then an option to save part of the population of the Milky Way, although it will demand significant resources and protection in order to keep it hidden from the Reapers and prevent them from following the arks to Andromeda. If you do create arks you should also have the duty of determining a portion of the population that goes on them. Be it race, skills, or other qualifications each choice is liable to have a significant effect both on your continued ability to fight the Reapers and the impact of what happens in Andromeda.
Alternatively, the protheans have demonstrated that, given sufficient power generation capacity and secrecy, it is possible to secure portions of your population in hidden vaults, safe from Reaper detection and assault. Obviously the prothean designs would need to be improved upon. This to would require significant resources and effort in order to protect it from Reaper detection. And again your choices about who would be preserved would have a direct impact on the future of the resurgent Milky Way galaxy, as well as your ability to continue your defense and mounting these projects. It is possible that during your work on these projects you might discover other prothean vaults with minimal survivors which you can repurpose while allowing the potential Rebirth of the proteins as a race.
As a third compromise option with significant risks and potentially significant payouts, you could make use of the Conduit technology. If you created arks with the minimum basics for intergalactic flight and launch them with construction crews and some equipment and supplies, as well as a Conduit receiver, on board, you could then supply and staff the arks to finish construction and population on route. This would allow you to divert additional resources to building vaults, although blindly sending people and resources on a one-way trip into the dark to unfinished vessels would would risk them being lost in accidents and other disasters.
The second game would be your rebuilding project. I would recommend 5 years post ME3, 10 at the outside, for your timeline. This will give you time for things to shake out, without ageing any of the characters too much. Also, it should probably be assumed that while the relay network was destroyed, relays not on the network, such as the Omega 4, geth telescope, and Charon relays, remain intact.
Personally, I am fond of your character being a prisoner on board a prisoner transport carrying all of Shepard's old buddies, Cerberus brass, Cat 6 members, mob bosses, merc bosses, interstellar rogues, and other assorted prisoners. After an accident, the prisoners seize the ship and run through the Omega 4 relay to hide in the debris field. Possibly this is simultaneously occurring along with the assault on Earth.
You determine the fate of the surviving crew and guards, including Ash’s sister, and defend the ship against adjutants, earning a seat at the table when the leaders of the various prisoner factions try to decide what happens next. The group will probably break into at least 2 warring sides, and, based on your choices as this character and Shepard, you will be able to help influence which factions join which sides, or fracture the prisoners into even more groups, up to it being every faction for themselves. The ship is destroyed in the fighting, and you and your group evacuate into the debris field. From here you and your group have to scavenge up supplies to survive and build a ship to get you back through the relay while fighting off the other factions, adjutants, leftover collectors, and any other survivors lurking in the wreckage. You would probably also have a struggle to take control of the ruins of the Collector Base which would vary depending on your alliances and whether the collector base wasn't fact blown up.
Depending on Shephard’s choices you would have possibilities for a number of interesting squadmates such as Brooks or Sidonis, as well as Ash’s sister. If the original squadmate is unavailable they would be replaced with an essentially generic prisoner, such as a Cerberus Trooper or a Blue Suns Centurion, Etc.
Depending on how it is set up this debris field section could be as much as a game and itself or simply a very protracted prologue. Either way once you and any companions escape back through the Omega 4 relay you are faced with a Galaxy reeling from the aftermath of the Reaper War.
The remnants of humanity have gone to war with the shattered wreckage of the batarians in order to recover any surviving slaves.
The hanar and drell are engaged in a multilateral religious war with themselves between factions supporting the traditional worship of protheans, The Collector Cult, and a religious reformation that is seeking to shape the hanar’s beliefs in the image of Javic’s opinions.
The drell homeworld has acquired a large number of Mass Effect craft from the Reapers, salarians, or someone and have burst out on the Galaxy on a crusade for power and resources.
The reemergence of a general higher in the chain of succession then Primarch Victus has left the turians deeply divided and on the verge of civil war, while at the same time aggressive moves buy Admiral Garrell and the quarian fleet have brought the risk of external conflict.
The quarians themselves are divided both regarding expansionism versus focusing on resettling rannoch, as well as the division between those who seek reconciliation and cooperation with the geth and those who would seek to dominate or destroy them.
The geth too are divided, as their growing individuality forces them into a number of camps, especially those continuing to search for reconciliation with the quarians, those who favor a renewal of war with them as the only path for self preservation, and the resurgent Geth Heretics.
Stung by the perceived betrayal of the other Council races, as well as many scientists and STG operatives, the salarian dalatrasses have initiated loyalty purges on their own populations, as well as renewed effort to strike against the Krogan and renew the genophage, if not exterminate the race completely. Rumors abound that they have also initiated programs to retaliate against the other Council races, even as refugees and resistance fighters flood to colony outposts and other sectors of the Galaxy.
Clan Urdnot continues to rebuild Tuchanka and expand to new colony planets, but is faced with challenges, both from conflict with the council races and others in the Terminus systems, as well as a newly unified krogan opposition based on Clan resentment of Clan Urdnot’s power as well as hostility to tank bred krogan, all possibly fostered by salarian intervention.
The asari, once hailed as the greatest and wisest of races, have been shattered, not only by the reaper attacks, but new revelations about the matriarch council's hiding of the reaper threat, which they had known for many generations, it's standoffish stance in the war, information about the justicars and the relative abundance and treatment of Ardat Yakshi, and the matriarch council’s triggering of wars with at least three powerful matriarchs: Samara, Aetheta, and Aria.
Aria herself is expanding her control in the Terminus, especially targeting asari bases such as Illium. While her mercenary armies have been somewhat depleted, both in the war on Earth as well as defections by those who desire to join the krogan opposition, the internal asari conflicts, or those headed to take part in the ongoing human-batarian war, she still retains a powerful core of troops, and with the acquisition of veteran Zaeed Massani to command her forces she has made great headway against her opposition.
The Yahg have also acquired space flight and our intent on unleashing themselves upon the Galaxy.
Depending on Shepard’s chosen ending there may still be Reapers floating around, especially in areas where the relays are no longer connected to the network. These groups would be unaffected by The Crucible Purge and would undoubtedly wind up in conflict with the surviving races, as well as the surviving Reapers who were either given organic properties or bound to the service of Shepherd. If Shepard died to provide organic elements to the Reapers this very organicness has shattered their unity and caused them to develop significant internal conflict. If Shepard bound himself to Catalyst and the Reapers, the melding was insufficient and the two have begun to divide with some Reapers following the Shepard consciousness and others remaining true to Catalyst, although both remain alien to unaffected Reapers.
Regardless of whether Liara was Shepard’s love interest, she has had brain sex enough times with Shepard that she has a little blue Shepard child of her own. Having continued her role as the Shadow Broker, she has been targeted for assassination by the Council of Matriarchs, driving Aetheta into open opposition, where she has rallied many asari Commandos to Liara’s cause. While Liara seeks to aid the Galaxy in rebuilding, she is focused on a new primary mission: to provide those members of the various war-torn civilizations who can no longer stomach a life in a Galaxy that has destroyed so much that they loved in taking flight in newly constructed arks to seek a new life alongside the Andromeda Initiative.
Shepard obviously is either effectively dead or blew out their cyborg parts in destroying all synthetic life in the galaxy and is now confined to a wheelchair in the care of their love interest. Nevertheless, Shepherd and most other gendered love interest have had one or more children, which in order to protect from Shepard’s notoriety the family has moved away from the alliance and into hiding.
Do to Liara's massive resources and connections, as well as her ties to a number of couples struggling with infertility due to either being of multiple races or other issues, she is currently also spearheading a project to help aid in fertility, especially for multiracial couples, allowing for the introduction of future mixed race characters.
A number of the other Normandy couples have children as well by this point, and, depending on Shepard’s choices, Javic will either have committed ritual suicide on his battlefield or will seek to rebuild a prothean race, either by finding other prothean survivors or just getting a date.
Perhaps the most significant source of conflict is the fact that the Citadel seat of the Galactic Citadel Council is now firmly ensconced in human space, leading to a clash over whether the Council or Alliance retain sovereignty over the station, and wherein in any dividers may lie, given Council space is now in orbit over the human homeworld.
As you emerge into this mess you will be able to work to try and aid projects or destroy them, build alliances or break them down, and help tip the balance in a galaxy once again on the brink of war. Depending on your allies you may be able to take control of various hidden mercenary, pirate, or Cerberus bases, and any troops or other bonuses therein to aid your missions. If you so desire you may even be able to carve out an interstellar nation for yourself and your allies, based in your fortress beyond The Omega 4 relay, although your ability to be successful at this will most likely depend heavily on the allies you make and the prisoners that Shepard has left alive.
The third game would obviously be in Andromeda. There has been a lot of discussions that are gathered here, but I will give a rough summation. Andromeda is severely fractured facing continued internal conflict among the Angara and the Initiative, with humanity on Meridian taking an increasingly more powerful role and challenging the might of the Nexus Council. In addition, the kett remain active, although factionalized, as their conflict with the Resistance and the Initiative is combined with a conflict over succession of the Archon. Into this mix we throw the issues of the Benefactor, the independent colonies, a rescue/recon fleet from the kett empire, and a influx of arks from the Milky Way, either from the evacuations as the Galaxy falls or Liara’s ark program for Reaper War survivors, not to mention the discovery of lost Angara colonies and the continued search for answers regarding the remnant Wars.
