It's been a while since I've seen it, but don't the nanogenes figure out how to repair people the proper way only after the doctor updates their 'template'?
The Doctor doesn't do shit to the nanogenes. Nancy just goes and hugs her child, admits that she's his mummy and will always be his mummy, and suddenly the nanogenes realize that they weren't supposed to turn everybody into copies of the child and instead repair all the damage they've done, including to the kid. The Doctor gives some explanation about how it came about from their comparing the kid's DNA to the mom's and realizing they'd goofed, but it's really illogical. Why would they suddenly realize the difference between the standard human DNA and the specific DNA of that kid just because they met someone whose DNA was
closer to the kid's than others'? Wouldn't they have realized it by finding DNA that was
more divergent from the kid's?
It's all just a justification for letting the cathartic "I will always be your mummy" line solve all of the episode's problems, just like the whole "human emotion lets the android overcome Dalek programming" thing was just a justification for letting the power of love save the world. It's absolute nonsense either way....
Absolute nonsense that I am just fine with, since I've always thought that character and theme are far more important than plot.
^Pretty much. It's just the normal Sci defending his idol thing...
I'm always amused at the claim that RTD is my "idol." He's not my favorite writer (though he is one of them), and he's not my idol. Joss Whedon and Aaron Sorkin are my writing idols far more so than Davies, and, frankly, I tend to enjoy Steven Moffat's work more than Davies's most of the time. And I've always thought that Paul Cornell was a better writer than both of them.
It's not that RTD is my idol so much as that I don't think he's a demon the way so many others do. He's a writer. Some of his stuff is absolutely brilliant --
Children of Earth, "Utopia," "The Waters of Mars," "Doomsday," "Smith and Jones." Some of his stuff is fun and enjoyable but not brilliant -- "The Sound of Drums," "The Stolen Earth"/"Journey's End," "Rose," "The End of the World," "The Parting of the Ways," "Last of the Time Lords." And some of his stuff is just utter dreck -- most of the first half of "The End of Time, Part One" (especially the Master's resurrection).
But he's not the hack so many people like to paint him as, and I get tired of people claiming he is.
Don't worry -- in a year or two, I'm sure that another group of folks will start claiming that Moffat is a complete hack, and I'll end up defending him, too, and people will accuse me of having a mancrush on Moffat and idolizing Moffat, too.

(And, in point of fact, you'll note that my prior post defended
both Moffat and RTD.)