All the other mess with Andromeda aside, I can't help but feel the biggest overall issue is that someone made the decision to take what was an interesting concept (exploring unknown space, worlds & setting up colonies etc) and careen it back to what is safe habours for the ME franchise (human protagonist come saviour of everything & everyone).
That's the thing, isn't it. They wanted to do a fun, feel-good, GotG-esque lighthearted story about this group of outsiders and misfits coming together and saving the day. And that's where the game is strongest, the characters and the squad interactions.
But they wrapped it onto an inherently gritty premise about space colonialism. If there was a one Mass Effect game that "should" be dark, should have hard choices and no win scenarios, should be grounded, shouldn't have a golden ending - it's a game with that kind of premise.
It's that pirates in Terminus pitch I'm always coming back to. That would have been a far better fit for the Firefly-inspired story Bioware wanted to tell than Andromeda was.