The whole 'lonely god' thing is just ehhh in general. I didn't hear anyone mistaking the Master for a deity, even when he had a beard. It ends up leaving the Doctor (and the whole concept of religon) seeming more pitiful than anything else -- even having characters mistake him for a prophet would be less cheesy.

DW has been taking digs at crooked clerics and badly organized religions since the dawn of time, but RTD seems to be saying that there is no chance of any faith being genuine in his universe and nothing is allowed to seem more godly than a vengeful, traumatized Doctor (unless it's an evil, scheming imposter, in which case it's slated to be defeated anyway). It seems a limited view at best.

*/rant* ;)