The plot was a total homerun

Let me fix the plot: The meridian needs to go. The Archon needs to go. The Angara are just another alien race, not some neo-synthetics that are artificially created. We go to Andromeda because we are hundreds of thousands of people who HAVE been informed of the Reaper threat in 2185 by our benefactors and private organizations, we keep the Kett but make them at war with the Angara over their right to certain homeworlds of Heleus. The plot revolves around helping both aliens and the Andromeda Initiative stop the spreading Scourge-pollution that is caused by Rem-tech and this involved a series of political intrigue between Us and them and the other them and how Angara don't trust us because the Kett betrayed them and started executing them, then went to war with them over their conflicts, even though Angara are the natives.

It becomes a story about colonization and not superficial bullcrap where true evil is defined or where there are religious cults that force people on their side to give us an enemy.

There'd be plenty of reason here, still, to kill wildlife like Fiends, outlaws who don't want any of the bereaucratic crap we brought with us on the Nexus, and many Kett and Angara sub-factions like in the game right now that occasionally need to be destroyed but also more opportunities for resolving encounters with peace. For example, they could've turned the initial "First Contact" protocol moment's mechanic where Ryder raises his hands into a consistent mechanic that we could engage in contextually and sometimes the specific group of Kett or Angara would react non-violently to it and let you scour around the vicinity without harm, and then upon doing stuff to the Remtech, the area would default to peaceful to the governing race of that area.

How much thought actually went into this game? Not much because it's fucking BioWare and their DnD and depassionated vet writers