2. The Remnant Are Protheans
It's essentially par for the course that your intergalactic menagerie of space politics and laser-blasters has an overarching power structure dating back thousands of years. For Mass Effect it's the Protheans, and to extrapolate further, the Leviathans and the Reapers. For the original trilogy, we occasionally dabbled into the history books to see how the former waged war with the Reapers, the story going that they were completely wiped out - aside from Mass Effect 3's Javik. ...Or were they? Andromeda's story is apparently focussed on another timeless entity known only as the Remnant i.e. something (or someone) that's been left behind. It's completely plausible that as their cities were falling, the highly advanced Prometheans managed to find a way to hop across time and space into the Andromeda galaxy, setting up shop with only a fraction of their populous. In fact, if you check out the original reveal trailer for Andromeda, you'll see some very Promethean-looking architecture sticking out the ground, alluding to where the plot may be heading. We know the doomed race had the technology to survive cryo-stasis, as Javik emerges unscathed 50,000 years later. That could be the same tech that's allowed a small amount of Prometheans to survive across the universe, emerging in a far more volatile and hostile state, thanks to fleeing for their lives beforehand.