>>1 With Ghost in the Shell SAC (and 2nd Gig), as far as the anime goes, I didn't really feel like I needed the characters' backstories. I felt like what relatively little they did show was enough.
The way I understood the ending of Code Geass was that Lelouch died, and his consciousness became part of the collective unconscious. C.C., being...well...C.C., was still able to communicate with him.
My big unanswered question is what's the story behind the gates and the false stars and the contractors and dolls in Darker Than Black. They don't ever go into that. It's part of why I was so frustrated at the 2nd season. They could have explored where the gates, false stars, contractors, and dolls came from, in addition to the evolution of dolls and contractors. It still frustrates me when I think about how they completely botched the second season and ruined its potential.