Series 3 started out on a high note, Smith and Jones, which suggested that the old, flippant Doctor who laughed in the face of danger would be able to survive Rose's loss; but by the end of episode 9, my affection for the Doctor had hit an all-time low. In episode 8 the Doctor had been distilled into an unappealing human persona - an inhibited creature of habit who treated Martha as a second-class citizen - but even restored to himself, the reconstituted Doctor we see in episode 9 is no better. Instead of rewarding Martha's loyalty with a deeper level of intimacy and communication, he silently embraces her. Instead of attempting reparations to the English villagers, the Doctor carries out a joyless and pointless series of revenges against the aliens that decimated them.
Reintroducing Jack Harkness in episode 11 was a breath of fresh air. In the face of Captain Jack's warmth and generosity, the Doctor's inflexibility becomes comical. Where the Doctor is helpless without his TARDIS (as in episode 10), Jack's willingness to spend the entirety of episode 11 lugging his worldly possessions on his back vividly demonstrates an alternative way of life, characterized by joy and spontaneity. In the new context that Jack creates, Martha's caring for her travel companions doesn't seem pathetic, just entirely natural and deserving of reciprocation. And the Doctor's discussion with Captain Jack about the fate of Saint Rose, so easily rewritten, makes it clear that his grief over Rose is no longer rational and is likely to be one of the factors behind his creeping calcification. I'm afraid that his ability to rely on Martha while still taking her for granted - the fact that in their partnership she gets to take on emotions, logistics, gruntwork, leaving for him the more sterile and scientific tasks - may be a factor as well.
If Captain Jack is a breath of fresh air, the Master is a hurricane of the same. Doctor Yana was more joyful, creative, and intelligent than John Smith, if less honest and less loving; and in his regenerated sprightliness, the Master is more alive and (I think) more appealing than the present state of the Doctor.
So I guess the question is, what does all this bode for the end of the series? Presumably the Doctor, helpless again, is going to have to rise to this new challenge by borrowing Captain Jack's nimble time machine, and hopefully some of Jack's attitudes along with it. He won't be able to pick on the Master the way he picked on the Family of Blood, either - maybe this will make him grow as well.
I still like the Master better, though. RTD's challenge in the next couple episodes will be to win me back.