Welcome to what is hopefully going to be a dev diary, from inception to full release.
While I get to grips with the Stellaris modding, I think a good place to start will be the Collectors. If I can figure out how to spawn a system near/at the galaxy core, I can begin working on the Collector state/country. I think the best way to represent them is either as an "empire" like the Vazuran Hegemony, or as a Fallen Empire with custom dialogue options, something akin to the Artisan Troupe diplomacy for example. Early game, as with the Vazurans, the Collectors would then raid the galaxy every now and then and be more of a background threat, while towards the mid-game they would start targeting colonies and planets, abducting pops.
Obviously the associated event chains need to be Mass Effect lore-friendly. Once I get a proto-Collector empire going and have some mechanics or a few events ready, I'll release what I have so far.