At this point, I expect, they already have an approved strong script, with a starting point, all major events, plot, and ending, and are just filling the blanks. Don't they?
Deadlines and resource management cause constant re-writes.
The immediate example that comes to mind that I don't have a link to is that the insider discussion that Star Child was originally only going to appear in certain pre-service histories (I don't remember if it was Colonist or Sole-Survivor) and that it was supposed to be a haunting memory of a child lost in said fight. When the budgets didn't allow a pre service history for every selected pre service, the Star Child story as universal to all Shepards regardless of chosen history was cobbled together in the eleventh hour.
Or, a better example and more concrete example is that much of ME3 was written with Javik being a companion intrinsic to the plot. When work wasn't finished and the corporate suits wanted to publish, Javik was excised and the some of the timeline was jostled around to try to make the game work without him. Once again, lots of big picture writing to be done in the eleventh hour.