They were never working on a 'contained story', there was a spinoff being developed actively alongside ME2 -- and which would have taken place concurrent to the main story -- that was canned. The idea that they had the "entire story" already written is PR bullshit. At one point, the reapers were supposed to align with Shepard to stop dark energy anomalies from destroying the galaxy. Parts of this storyline are still in the game, btw. Specifically, in ME2, dark energy fucking with things is mentioned quite a few times(that you've probably already forgotten) and it's never followed up on.
Also, there was originally a somewhat-similar ME3 ending would have been less ridiculous and more sci-fi. The crucible would have been based on real world physics rather than space magic. I guess hiring a physicist to help flesh the idea out was too much for EA so therefore space magic.
essentially, they wrote themselves into a corner due to time constraints, shit writers, and having too many cooks in the kitchen.
Additionally, most of the reason Andromeda is so subpar is because of how much of it was cut. At various points of development they had things like manually piloting your ship between planets, dynamic weather/environments, etc., Not to imply that they would have been good features(who knows), but that is a lot of wasted time and effort.