There are many examples of writers making it up as they go (Stephen King's Dark Tower cycle, Wheel of Time, Song of Ice and Fire, even Lord of the Rings), it's just a matter of writing talent and priorities.
The entirety of ME2 was basically a waste of a game, focusing so much on characters that the overall plot got completely lost and was never furthered. Hence, enter the MacGuffins and Deus ex machina in ME3.