That's just sparked off a thought in my mind! (a quote by neardark, saying how they liked the idea od redemption)
Perhaps Boomtown was encapsulating the series (or the story arc) as a whole, into 1 episode (bear with me!

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We all have suspicions that the Doctor has done something terrible, and in his attempt to run away from it has only made things worse (time war).
Boomtown showed this perfectly - the Slitheen had done something terrible - she teleported herself out of No.10, but left her family. The Doctor, we suspect, fled the time war, and left the rest of the Time Lords to perish.
Throughout the series, the Doctor has also been reckless - blowing things up and letting people die, just so he was OK. This is what the Slitheen planned to do - destroy the Earth so she could be with the rest of her family. However, she was stopped and was given the chance of redemption - another crack at life.
Perhaps this is what will happen in the final two episodes - the Doctor will have a chance to get out of the mess he's in, but it will have grave consequences for a huge number of people. He decides not to take the opportunity, and is rewarded with another shot at this life: instead of regenerating into the 10th doctor, things go back (like the Slitheen into its egg) to the point where Paul McGann regenerates into David Tennant.
And the Bad Wolf - well, that is the Doctor. He is destructive for his own personal gain, but is given the chance to redeem himself.
(Usual speel - hope this makes sense; 3 in the morning etc.

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If this turns out to be true, I will be seriously shocked
And if this has been posted before, then sorry - the (4th June) thread's just too long to read!!