Try LiSaT. The main character is a bit obnoxious, though. Black kid who thinks he's Jesus. (Which we all know is impossible since there are no black people with powers beyond the ability to say nigga interchangably with any other word.) The ending is interesting though, really makes you think.
I enjoyed Elfen Lied when I watched it, but that was a good while ago. I'm not sure what the ending was as I never watched to the end of the series, but the intro was amazing, plus there's some gore and nudity so there.