I guess to me the main story plot fell off the rails when they changed the direction of the story after losing several writers but what they lost in their main story focus was still executed nearly perfectly in their character focus.
That's the problem - I don't think they HAD
main story focus. They apparently hadn't nailed down the motivations and backstory for the Reapers by the time ME3's script was started, because they toyed around with Drew Karpshyn's nonsensical dark energy plot, then cobbled together the basics of the "machines kill organics to keep them from being killed by machines" ends we got. Hell, Mass Effect 2 and 3 are at their most coherent when the Reapers aren't really the main focus of the story.