Even though I haven't played KH3D yet, I think it's pretty safe to say that Days is (by far) my favorite KH game.
You get to see what goes on with the "enemy" for once. It gives you a chance to relate with the antagonist. For this game, the bad guy is the good guy.
I think that's also why Death Note was such a great anime for me. But in the end, both of them had intentions to help everyone. The organization wasn't really that bad. They just wanted their hearts. Just like with Light, he wanted to rid the world of evil.
I may not know everything since I haven't played DDD, but I know enough to know that it wasn't purely evil intentions.