But what if there IS a "chair agenda"? What might it be? After collating all the data, I've arrived at the conclusion that yes, such an agenda exists, and it is this, my friends: Heroes stand, villains sit. Make no mistake, Doctor Who has always been about standing. Standing up for what's right, and so on, but the Doctor also travels in a ship with no real seating. This is no USS Enterprise where everyone wants a shot at the big chair! Our heroes operate the console standing, the better to run when it's time to spring into action. Taking only the first story of Series 9 as evidence, Missy is found sitting. Davros always sits. And when our heroes are offered chairs (in a plaza, on Skaro), it is always to compromise them. Clara becomes Missy's "companion" after she sits down with her. Davros is trying to get the Doctor to sympathize with him, to combine the Time Lord's energies with the Daleks'. When the Doctor sits, he becomes more like Davros (and even gets to ride the wheelchair).
If we look for chairs, or the absence of chairs, across the rest of Series 9, a pattern develops. I'm not talking about evil ghosts throwing chairs in an underwater base, though you can count that as supporting evidence if you like, but skip ahead to The Zygon Inversion. First, we have Bonnie taking over Clara's form, relegating Clara to a dreamscape. The only way to communicate with Bonnie is to sit in a chair in front of the television. That connects her to the villain. The chair does.
And when heroes die, when they must Face the Raven, they die standing.
In Heaven Sent and Hell Bent, the Doctor does a lot of sitting, granted, but as he says himself, he's no longer "the Doctor". He's too wrathful, having suffered one loss too many. When he sits is when he's most thinking about that loss, or else Clara's picture wouldn't be on the wall.
It may have started as a joke, but you can't tell me the show doesn't actually have a "chair agenda".