1. a) You're assuming that Davies is trying to upset people when it seems that what he is doing is celebrating people who are not often celebrated. If one feels personally attacked by someone else getting the attention, then one is seriously immature. 1b) The show is for children, who paradoxically aren't as immature about seeing people who aren't like themselves. Children themselves are not as set in stone about what "normal" is — particularly not sexual identity — and therefore do not think anything is particularly weirder than anything else. It's gross when everyone's parents' kiss, for example. 1c) This back-door "go woke, go broke" argument is widely and easily discredited as conservative wishful thinking (with a rhyming scheme).
2. If Doctor Who's original mission was science education, that was lost in the mix in the first season. As a fan since the 1970s, I can say that it's basically always been anti-fascist science fiction, and there's a reason the Dalek creators (the Kaled) dressed like Nazis. There was a line in the latest special where the Doctor corrected Ruby that what he was doing was a science and she countered with a paraphrasing of Arthur C Clarke: sufficiently advanced technology is indistinguishable from magic.
3. This is not where it gets fun. What about this show turned you into a progressive 40 years ago? Watching white people run around with other white people doing white things in white London? Was it the overtly sexist way that Leela paraded around in a leather skirt or was it episodes of the overtly racist Talons of Weng-Chiang? Did you feel included by the space virus trying to eat the Doctor's mind in "The Invisible Enemy"?
4. Every one of your examples of the Doctor giving up power that he did not actually want in the first place. That's not sacrifice. That's power brokering. He doesn't want to be president of the Time Lords — and living on Gallifrey — because he wants to run off and do his own thing. Running off was what he wanted to do, and if he was sacrificing he'd do what he didn't want to do for the sake of others. Donna, as you noted, did, in fact, give up something she wanted. Not wanting it means it's not a sacrifice. It's OK to regret sacrifice even though you know you'd do it again. And recognizing that is not a sign of brain damage.
5. (You wrote a second 4 after calling people stupid, but I'll call it 5 for you.) The idea of justice has always evolved, and it evolves faster now. There was a time when it was OK to own other people. It is now considered a bad thing. Freeing enslaved people used to be a criminal act; now it is considered at the very least justice to capture someone who enslaves people and put them in prison. That's just an easy example that you can't argue with. In America when Doctor Who first aired 60 years ago, some people considered it perfectly acceptable in many states to have racially segregated public spaces — places where Blacks weren't allowed to use the same water fountains and public pools. Places where they had to enter through the back door so they wouldn't be seen by white customers. The thing that pisses off right-wingers about changing the notion of justice is that it often moves the goalposts to put them on the losing side of things. If your great grandpa thought Black people should sit at the back of the bus if they were going to be on it at all, then he gets made to be on the wrong side of modern thinking. And he gets mad about it. And he thinks how much better it used to be in the old days. In the old days he was happy and didn't have to consider other people's feelings. He didn't have to worry about Justice because it was whatever he thought it was at exactly that time and how dare *they* change it around him. Of course, what has happened is that the cruelty of the status quo has been reveled to enough people that they have said "actually, let's not behave that way anymore because of observable outcomes of that behavior." And, collectively, eventually, the notion of justice changes over time. Now imagine a Time Lord being slightly ahead of you on that curve.