What gets me is that you can change the past except when you can't. They've tried to explain it away using "fixed points" which can't be changed but even that doesn't hold together.

For instance, the Doctor just admitted that he could change things that he thought he couldn't change and 1) brought back Gallifrey from the Time War, and 2) brought it back into our universe prevent his death. If I were him, this would be the point where I'd say "Maybe I should go and see if I can bring back Rose's father too. Then I can start on Astrid, and maybe that girl from Waters of Mars".

And Gaiman's episode was bizarre. he had the Tardis acting like a stereotypical wife when at the same time the Tardis crew included an actual husband and wife and they didn't act towards each other like that. And if the Tardis is sentient there's no reason he couldn't hook a voice box into it, except that doing so, thus actually following the logical implications of the Tardis being sentient, would mess up the rest of the series. That episode was just a blatant case of someone wanting to write his pet fan theory into the show and getting to do so because he is Neil Gaiman.

The series also takes a negative attitude towards immortality, despite the Doctor living for a long time.

I'm also sick and tired of the Doctor deciding that a problem whose only obvious solution is violence and killing can be magically solved if he just refuses to accept that the solution is violence and killing. In the real world, such a policy would lead to even more killing.