that was interesting. i liked it, but there were some confusing bits...
1. the extra regeneration energy that they gave matt smith's doctor now makes no sense.
2. if the jo martin doctor was pre-hartnell, why did her tardis look like a police box?
3. kinda weird that she chickened out, but was willing to let the old guy kill himself and the master.
4. NO ADDITIONAL APPEARANCE OF JACK?! THAT'S UNACCEPTABLE BBC!
5. edit: why does the doctor have the same physiology (two hearts) as the shobogan?
This is, actually, the first Chibnall-led Doctor episode that I actually was excited and/or fascinated watching. All others have been more like intellectual exercises and child-teaching episodes (everything from race relations to plastics in the environment). This is the first actual contribution to the Doctor's mythology, and what a doozy it was!
Personally, I find the return (and return . . . and return . . . and return . . .) of the Cybermen and the Daleks to be boring as shit (and now, The Master [though this is the first time I really felt the Master was
creepy and threatening, and disturbed, not just disturbed]). There have been so many "the world is going to end" moments with each of them, that there is no story-telling tension: of COURSE the Doctor is going to take care of them somehow and at some point, because there's never NOT been a time where s/he hasn't! But with less familiar or new threats, that track record isn't present, so the investment is present.
All of what you posed are very good questions. And the first one I'd thought of also. My thoughts on what you wrote:
1. Matt Smith's Doctor never needed the regeneration energy to regenerate again, but the Time Lords - to keep him/her/it from discovering that he/she was actually different from every other Time Lord, sent it along as if it was needed, in order to maintain the illusion. That, of course, voids 100% of the tension of that in re-watching that episode. In addition, it throws into question whether they actually thought The Doctor DESERVED 'additional' regenerations, if they knew that he would regenerate anyway. (i.e. Their sending the extra was a cover-up, NOT a decision based on merit which is how it played in that episode.)
. Of course, it could also be that, when they were gene-modifying the entirety of the planet, they modified the 'proto-Doctor's' genes to limit her regeneration. But that seems less likely (as it seems it would have been far more difficult to fine-tune her alien genetics than to add a new plasmid to everyone else's).
2. I missed that.
3. Possibly it is like someone who believes in the death penalty, but who would personally be unwilling to actually pull the switch. She just couldn't bring herself to kill her old friend, but basically, with what he had now done, she knew he could not be allowed to continue.
4. Agreed. Jack's popping in earlier in the season to warn, "under no circumstances give the McGuffin over!" just screamed that he'd be back to help get the Doctor out of it in the end. The fact that he wasn't was a let-down.
5. My thought (based on assorted SF I've read) is possibly that the being that became The Doctor - when passing from its prior existence/reality into this one - took on the biology of the most comparably-intelligent species nearby. It may have had, in its own dimension, NO physical form. So it created what body it needed when it arrived.
. Another possibility is that s/he came from an alternate version of Gallifrey, in which all of them already had the capacity to regenerate. But I like my first thought on that better... oddly it seems more likely.
. Of course, unless they say any of that in the series, that is 100% my justification for the unlikely coincidence of them having the same biology.