I agree I don't think it was planned, but most of the history and lore of the show has been made up as we've gone along. The idea of regeneration itself, most obviously. I'm okay with that, by and large, as long as it stays more or less interntally consistent despite it.
Empty Child has got to be one of the two, right? I thought Blink was excellent as well, so was Eleventh Hour and The Time of Angels. Girl in the Fireplace was a bit overrated, imho, and Silence in the Library let down a little by its second part, but both were nonetheless the pick of their respective series.
Over the piece, there are a few things that rankle, and his era as showrunner hasn't been what I'd hoped. He's run out of ideas a bit, had too many balls in the air in the story arcs, and it's all generally got a bit messy. But I prefer to look at the positives - written (and then overseen) some terrific individual episodes; cast at least one, perhaps two, great doctors; and maintained the popularity of the show and secured its future.
Interesting idea, and a very plausible one. If I ever get round to watching those episodes again I'll see how it fits.