IMO the show is too far gone. Moff has kind of wrecked the continuity of the show, so I will just say what I would have done at the start of the Capaldi era instead.
In Capaldi's first series I would have kept Jenna on. You would have needed her for 1 year to help ease in the new Doctor. Also I wouldn't have written her that way. I'd have let her be herself more, made her less smug, not had her slap the Doctor or done any of the she is a better Doctor crap. I'd have had her leave at the end of series 8 however.
As for Missy well. I'd have made Missy the time lord Clara that we saw in The Name of the Doctor that told Hartnell what TARDIS to steal. I'd have revealed that she survived the time war, but regenerated into Michelle Gomez.
Now Timelord Clara was desperate to help the Doctor as that was all she had been created for. So she decides to download the minds of all the people he failed to save into a virtual heaven to live forever, and thus wash all the blood off of his hands. She'd also be punishing evil people he met on his travels by downloading them into a virtual hell. I'd also reveal that she was the woman in the shop who had brought Clara and 11 together so that she could be born.
IMO that would have been a better finale and story. You'd have had the Doctor discover the planet she had set this new matrix up on. Missy/Clara would be burning up one star after another to power it (but wouldn't care as all the minds of the people she killed would be downloaded into "heaven")
You'd also have a scene where the Doctor visits the matrix and maybe meets people who died in previous stories like Lynda with a Y in the heaven, and past villains like Solomon the Trader who'd be suffering in hell, and had been for hundreds of years. Also the twist is that Danny would be in hell because of what he did during the war, with the timelord Clara obviously having no affection for him.
After Missy/Clara was beaten, Clara would leave. In series 2 I'd use Journey Blue and Osgood for 12's companions. Both would be good as Journey would be n aggressive Leela style companion who could clash with the Doctor, whilst Osgood would be a Jo Grant, Susan type that would look up to him like a daughter. Neither would be romantic however.
I'd have Journey and Osgood clash at first, as one is a gentle scientist, the other a hard mercenary, but both would bond over losing loved ones to the Daleks. Journey obviously lost her brother, whilst Osgood I would reveal lost her mother to the Daleks. This cute chick here from Resurrection of the Daleks called Laird who was shot by the Dalek duplicates.
Laird, Doctor Who I'd reveal that she was Osgood's mother.
Lets be honest Laird looks exactly like Osgood, dresses like Osgood and acts like her. I'd reveal that it was her death that inspired Osgood to join UNIT and led to her admiring the Doctor for always stopping the creatures that had killed her mother.
I'd also bring the Master back in series two, but HE'D be written like the Master and played by Simon Templeman. This guy here.
https://youtu.be/qi86yeXB9pII'd have Osgood and Journey leave after Capaldi's third series and bring in a new companion who would be from the year 100 trillion. I think it would be interesting to see a companion who was from a time when the stars had burnt out and had to live a miserable existence in a cold, dead world, struggling to survive, journey to when the universe was young and see planets like the earth that she had only heard about in legends before.
I'd cast either Alison King (the babe from my profile pic) or Morven Christie. She played the cute nerdy girl O'Donnell who was a fan of the Doctor in that Peter Capaldi story with the ghosts, that got killed by the Fisher King. She's a brilliant actress.
Finally I'd also make the Capaldi Doctor more like Capaldi himself. Capaldi in real life is a lovely guy. He's nice, charming, loves children and TBH I think it would have been better in hindsight if 12 had been that way, even though initially I liked the darker take on 12.
It was kind of obvious to have a guy who was known for playing villains and angry people play the Doctor as the angry dark Doctor. IMO having 12 be the nicest and softest Doctor would have been more unexpected, in much the same way as Jon Pertwee, known for being a comedian, played the most serious, straight forward Doctor, and Matt Smith the youngest actor, ended up being the best at capturing his great age.
I'd still make 12 serious of course, no wacky crap, but I'd have made him the most compassionate which actually would have been more different to 11 and 10 who were both more ruthless and more in keeping with Capaldi as a person.
After Capaldi had done 5 years I'd move on with him and hand over the show to Iank, Mott, Rawkuss or anyone else here LOL. I'm sure they'd do a better job than Chibnall sadly. I'm basing that on his "a woman isn't ruled out from the role" UGH a female Doctor should never be considered IMO, same way I'd never consider a man for the Xena reboot.
Not a good sign as it shows that not only might he do it, but that he isn't telling these feminist fans to go fuck themselves which he should. Pandering to feminists is the first sign of a show's decline IMO.