As soon as The Master's plan was set up using a Paradox Machine, surely it was clear that the actual events of the takeover would be undone once the paradox was undone. However, it wasn't a complete reset button, because the characters themselves have been significantly changed by this.
Doc 10 was already showing a darker side than most of his predecessors, and that will surely only become more acute as a result of finding another Time Lord, and then being left alone for the second time (or is he?).
Martha has grown enormously over the season and particularly this final arc.
Martha's family have been left devastated by what they have seen, and only Martha to share it with as the rest of the world is oblivious to what happened.
All this talk of deus ex machina (or plural of) is somewhat disingenuous as well ... the Doctor has been shown on a number of occasions, not just during these three seasons but before, to have some level of psychic ability. It is perfectly consistent with that to have him spending his year of captivity tuning himself into what The Master is doing with the psychic signal over the people of Earth and using it against him.
Yes, the "divine" Doctor was a little over the top, but then how many hundreds of other things across the history of Doctor Who could you level the same accusation at?
For me, this was the most satisfying season finale of the new series so far, and leaves us at an interesting point ... the Doctor is alone again, but having changed as a character through a companion that he fell in love with, and another who he knows fell in love with him, but he treated badly.
The earth has also changed because the timestream was reset to a point after the presence of alien life had been confirmed to them live on television ... not to mention the assassination of the US President by them.
And suddenly everything the Face of Boe said and did over his three brief appearances in the show makes sense.
And the Jack Harkness we will see in TW season2 should now be able to come to terms with his immortality and be a better character for it.
Most of the criticism I have seen for this episode has come from people who just don't like RTD's take on the show and the character of the Doctor. That's unfortunate, but the ratings, and Audience Appreciation figures for his tenure as Exec Producer show that that is a minority opinion.
If the BBC wanted DW to become a powerhouse, critically acclaimed family SciFi (rather than SF) drama that would own Saturday evening television then he has delivered big style. And good on him. I (along with my wife and children) will definitely be with staying with him for the ride.