I do wonder if Gaiman's ideas were more expansive than the budget.
I don't necessarily think Gaiman is necessarily some uber-writer who can do no wrong but I wonder if some of his ideas were let down by the production itself. Was the comical castle meant to be more of a park attraction? Were the kids forced upon him and so on.
I don't know. I know he felt a bit stiffed on The Doctor's Wife by them using the Ood rather than a new creature he'd dreamt up, but on the whole I'd imagine Gaiman would have much more latitude than many of the other writers. In the same way RTD never meddled much with Moffat and Cornell's scripts I can't imagine Moffat would tinker much with Gaiman, or give him a really strict brief.
As for the kids, well maybe that was Moffat's idea, or maybe Gaiman wanted children then Moffat suggested Clara's kids?