The premise is arguably silly, but I don't feel it's the issue itself and they could have told a far more compelling story hitting its own unique narrative beats under the umbrella of the Andromeda Initiative. It's just a shame they didn't, and relied too heavily on derivative science fiction tropes. It's like they pushed too far ahead of themselves, not content with keeping the story of the Andromeda Initiative itself and the immediate challenges it faces upon arrival in a truly uncharted, alien world, and instead wanted to fast track the situation in Andromeda that would allow them to tell more familiar stories with established factions and leaderships, outposts and worlds, and comfortable conflicts.
If I'm going to armchair critique on how this could have worked, the game should have double downed on the risk of the initiative and the emotional claustrophobia of the setup; Hyperion arrives in Andromeda, there's the presence of the Scourge and disrupted habitats, zero contact with all the arks and the Nexus, with an emphasised sense of loneliness and survival. Don't rush into new species and ancient alien technology so quickly. The premise disconnects you from the Milky Way, open with disconnection from the Initiative itself, and explore the implications of that. Make the discovery of the Nexus and the arks major events. First contact with a sentient alien species a huge narrative milestone that comes at a surprise later in the narrative, not within the first 20 minutes. Scrap the Remnant tech; planets unpredictably hostile and lonely. Explore the blooming stress in the Hyperion crew due to the implications of being totally cut off and lost from everyone. Tell the story of the Initiative piecing itself together, through exploration of this totally uncharted galaxy.
EDIT: And as I've said before I think the absence of an omnipresent key narrative theme driving much of the story beats does a huge disservice to the production itself. Each game in the trilogy has one, even if execution varies. Mass Effect 3, flaws and all, always keeps the war at the forefront no matter where you go or what you're doing. It's the governing thematic device giving purpose to the hero, the supporting cast, the state of the galaxy, and the background ambience wherever you go and whatever you. Andromeda doesn't really have anything like that. Too relaxed, flowery, and scattered.