If you look at the series the right way, it's an epic struggle on the part of these badly-broken people to fix the world, to do something about the problems which made them the way they are, rather than erase it (Third Impact) or perpetuate the status quo (who knows what Seele's goal is, but rarely do unpleasant old men want anything that's good for anybody else). They do this while fighting an enemy who would kill them all and pretending to serve the other while subverting Seele's resources to their own ends. It's a tightrope.
That's a powerful story. By its nature, it's going to be full of misery and intrigue and death and broken people being terrible, heartless bastards to each other and themselves, and the plan can only succeed if most of the players don't even know it exists. Bad things are going to happen to everybody. And then at the end... they win. They actually pull it off. All that misery and death actually meant something. They not only beat both their enemies but achieved something to help themselves and make sure nobody else ever had to go through that.
But you'd never know from what shows up on the screen.