I have confidence that BioWare will be able to explain any and all questions that we may have. They have always been the masters of RPG storytelling and shame on you all for doubting them.
Here's my take! *fwoooosh!*
The first three games were actually just military simulations run by a super-advanced super-computer with a power ego trip, installed on board this new supershipcolony or whatever. The power ego trip explains the self-insert mary sue robots (the reapers, the geth, Saren AND Shepard's transformation into cyborgs (since robots are superior to organics) and why everybody ONLY wanted to fuck a computer program with Tricia Helfer's voice once it had a cameltoe installed, or a robot body with a cameltoe to be exact).
The simulation was meant to find out how the universe would fare in a war against a super powerful enemy! Because the super-computer didn't have much military knowledge it drew inspiration from a number of popular video games and science-fiction movies, like Contra, Gears of War, Starship Troopers, 2001: A Space Odyssey, Starship Troopers, Star Trek, Starship Troopers, Star Trek, and Lolita.
*cut to a scene with Keith David voicing a black guy who may be kernel or general or something talking to New Shepard*
New Shepard: "Man, that was some freaky military simulation! At least I got laid several times."
Keith David's new black military guy: "New Shepard! We have to talk! The egg-heads over at the super-computer lab is saying the simulation may NOT HAVE BEEN JUST A SIMULATION!"
"I'm getting laid for real?!"
*awkward animation of Keith David smacking New Shepard in the face*
"Dammit, New Shepard! That's not what's important, New Shepard! It turns out it wasn't simulating fantasy warfare! It was showing us a glimpse of THE NEAR FUTURE!!"
"I'M GONNA GET LAID IN THE FUTURE!"
"UNLESS THE EVIL SPACESHIP ROBOTS KILL US ALL FIRST!"
"I DON'T CARE I'M GONNA FUCK A BLUE CHICK, A CANADIAN GUY, A TEST-TUBE WOMAN AND A LADY WHOSE BODY WAS ALL TATTOOS."
*movie trailer guy (not the dead one): "MASS EFFECT ANDROMEDA - MASS EFFECT BEGINS. FOR REAL THIS TIME."
There. Plotholes solved, or shall we say UTTERLY DESTROYED AND HUMILIATED!? See how easy that was for me? BioWare will no doubt do MUCH, MUCH better than me.
Have faith, ye of little faith!