One of my favourite things about the Ar tonelico series is that you can’t dodge the consequences of your actions simply by being the protagonist. You are held accountable to the same moral standards as the enemy, and you can’t just get away with the end justifying the means. Sometimes both sides look like the bad guy, and the game doesn’t try to excuse your side just because you’re on it.
The first game has a little of this, but it was downplayed because the story doesn’t revolve around political factions as much as the second game’s does. AT1 hints at it in the beginning, but you don’t see it really blossom until the end of the game. I think in AT2, the story’s genuine acceptance that both sides have a sincere point, and neither is pure evil but neither is perfect, has finally come into the spotlight.
I’m a big fan of that approach. When I was a kid I didn’t really notice, but nowadays I can’t help being critical of games that oversimplify and let the heroes get away with being as callously destructive as the enemy. Most RPGs tend to let that fly (other than the Suikoden series, which as far as I’m concerned is in a class of its own w.r.t. understanding of politics, morals, and the human heart), and I’m used to putting up with it, but it’s truly refreshing to see a game that applies a consistent set of standards to everyone in the story.