My understanding is that Moffat suggested (not asked) that Jenny should survive simply because the audience would assume she would die, so it would be more surprising.

I loathed this story on broadcast and again when I rewatched it when going through Doctor Who in order. Not only did I find it slow, boring, uninspired and illogical (poor world-building, rubbish science, plot holes you mentioned), it seemed to chicken out of the real issue here, the Doctor's paternity. Jenny is not Susan's mother. She is not really the Doctor's daughter. She is the Doctor's clone (so... shouldn't she be male? Perhaps not, now we know Time Lords can change gender), forcibly taken from him. The story was commissioned specifically to show writer Stephen Greenhorn that the Doctor could change, yet the events of the story have no lasting impact on him (the Doctor, not Stephen Greenhorn), not least because the story is followed by a comedy episode. It seemed to sum up the creative drought I found the series in at that time: repetitive, boring and not following through on its promises, with shoddily-crafted arcs and no character development. Looking back at my review from original broadcast, I see I also objected to "macho posturing" and Tennant and Tate shouting instead of acting; I had largely forgotten this, but the "I never would!" speech lingers on...

I may well re-watch new Who in order later this year and it will be interesting to see if my opinion has changed at all! I have mellowed recently regarding some stories I saw as clunkers, new and old. But I suspect this will remain a clunker.