One thing that I hated (HATED) about the later years of the new series under RTD's guidance was that the Doctor was portrayed as being a bad person. His own doubts and fears about himself were read as being wholly accurate, and Davros's words were repeatedly shown to be more or less accurate.
Having the main character(s) become self-loathing and ashamed of their actions seems to be a trait common to RTD's shows. For example, Children of Earth was probably the most involved RTD's been with Torchwood. And it was in Children of Earth that we see the characters basically be self-depricating the way the Doctor is. Hell, Gwen's opening monologue in part 5 about how horrible humanity is basically sounds like something the Doctor would say about himself in the RTD era.