The thing about it is they've written themselves into a corner. Both the original and the current motivations behind the Reapers would imply that there
is no hope for ever resolving the issue in a favorable manner. You'd either crush organic Galactic civilization permanently, crush all Galactic society to become unrecognizable in a new dark age, or you'd allow the Reapers to continue with their cycles thus extinguishing the entire point of the games. In essence, all three games and the stories that they tell are pointless. They build a false sense of heroism and hope, only to completely crush those feelings and replace them with utter contempt for ever wasting time with such a misguided conception of reality.
The story ultimately doesn't foster positive thoughts, only negative ones. From the very beginning I've found Mass Effect to be a story that paints a picture of a small glimmer of hope, the immeasurably minute chance of success in the face of insurmountable odds. Mass Effect 3's ending, the final 10-20 minutes of the game, completely eradicates those dispositions. It ruins all three games for me, and makes me never want to play through any of them again.