The Doctor: Excuse me. Do you mind not farting while I'm trying to save the world?
The Doctor: I can't believe I'm here to see this! This is fantastic!
Rose: Did you know this was going to happen?
The Doctor: Nope!
Rose: Do you recognize the ship?
The Doctor: Nope!
Rose: Do you know why it crashed?
The Doctor: Nope!
Rose: Oh, I'm so glad I've got you.
Chosen answer: 1) When Stephen Moffat took over he ignored a lot of what had been developed before (there is not in-universe answer). 2) It would have killed Rose, so the Doctor absorbed the energy. His body regenerated before the energy could do a significant amount of damage that would prevent regeneration.