Next Mass Effect: I see heavy retcon of ME3 ending + reunification with andromeda

There will always be Krogan and Quarians in any world state. The Geth have already shown no intention to follow Quarian survivors around the whole galaxy in an attempt to kill the last one off and Krogan will always keep searching for a cure whether Shepard helps them or not. These decisions only mean that the species probably won't be on the forefront of any conflict in any future game, but they'll always be there, so these aren't really that critical for the future games. Anyway: I expect BioWare to pick the world state they find the most interesting to tell the next story and don't even attempt to continue with save file imports of ME3. The next one will likely be a story with a clean slate for every player. 

If it's set far enough in the future, the squadmate choices won't matter much. You could make some choices on the gender of your Shepard, LI and so forth. They could even do a world state import so you don't have to bother with that. Krogans don't have to be off the table. It's not like they vanish just because the genophage continues. They live to be 1000 years old. Including them wouldn't be a stretch. Even quarians could be worked in under any conditions if you assume not all ships were dumb enough to engage the geth. Then, too, the geth could be rebuilt and it's fairly unimportant as to whether or not they're the "original" geth, since only Legion had a personality.

The biggest decision would be regarding the Reapers. RBG & Refuse. I thought I'd read somewhere that Destroy was the most common option, but I don't know what that's based on. Similarly, Liara was the most common LI, and there she is. Though, honestly, Refuse isn't off the table. Sure, there are dead Reapers, but that happens no matter what. Who's to say members of MW races didn't go underground and resurface once the Reapers were gone? Asari and krogan could certainly wait that out and care for other races who are playing popsicle. Synthesis would be the least likely because it's too obvious. I say Destroy but I guess we'll see.

Edited to avoid wall of text.

Man, I think the rachni just vanishing through a relay is more believable than the krogan ever just agreeing to work with them.

Lines fade in time. Or were just symbolic/metaphorical for the ending to show it had occurred.

Probably some kind of wetware connected to whatever network the Reapers and the brat were hooked up to. Though it's hard to tell when presented as such dumb, pseudoscientific vagueness where the trees get circuit boards and everyone lives happily ever after because.....reasons?

Even beyond the details, the premise itself is so fundamentally stupid, in that it falsely assumes conflict stems from misunderstanding rather than conflicting interests.

And also that solving the organic-synthetic problem somehow has anything to do with 90% of the plots and subplots we experienced. I mean aside from the geth Heretics and that one AI on the Citadel in ME1 we ran into, AIs basically didnt feature in the the hundred other belligerent conflicts between Council/Non-Council/Krogan/Turian/Salarian/Rachni/Batarian/Human/Quarian/Corporate interests/Biotic Extremists/Ancient Plant Lifeforms/rival gangs and mercenary groups/terrorists/slavers and pirates/crooked cops/political and ideological factions.

How the green beam solved all those issues I don't know (besides brainwashing), but regardless, it doesn't make for a good setting in terms of narrative or thematic potential.

Not least of which is, assuming free will is still a thing, how do people react to bring "upgraded" without their knowledge and consent?

I've been researching Stargate SG-1 and there is an early episode where O'neill absolutely loses his sh*t when he discovers that his consciousness has been transferred into an Android body that perfectly resembled his own flesh and blood form. It didn't matter that this form was stronger, more durable,etc. This was a personal violation and not was he p*ssed! Now imagine that in a galactic scale.

Who said the green beam did solve those issues? The Catalyst wasn't tasked with finding a solution to those problems, and the peace we see in the epilogue slide is  achieved in all endings due to the races working together so it's not Synthesis that caused that. 

Yep, Wreav got brainwashed for sure. Whole of the genophage arc he is ranting and raving about punishing the galaxy, but the green alters his brain.

His thought process had nothing to do with understanding synthetics or whatever. Guy just wanted revenge on some other organics, but the green beam rewrites him.