I'm writing this after seeing End of Time, so some of these may have been answered and I just missed it.
In series 1 (2005) Margaret Slitheen said "Playing with so many lives, you might as well be a God" in Boom Town.
In Parting of the ways, Rose said "I want you safe, preotected from the false God."
Emperor Dalek said, "Hail the Doctor, the great exterminator."
Obviously, he killed the Time Lords in the War, and sent them to their deaths in End of Time (or sent them back to their deaths).
Also, Rose said she couild see "all that is, all that was, all that could ever be" or something like that. And she brought Jack back to life.
What if she scattered herself (her regenerations since she was POSSIBLY at least part Time Lord?) through time, as his future companions, to keep him safe from the false God (going back to Margaret).
Also, in Runaway Bride, Donna said "sometimes you need someone to stop you."
My theory is that Rose saw herself leaving the Doctor (dying in battle) and sent him protection, while she was a Goddess.
Also, how come the Doctor could leave the Time Lock after the Time War? Also, in Dalek the single Dalek fell through time, the Emperor my ship survived falling through time, crippled but alive."
And Dalek Caan entered the Time Lock to save Davros.
Why did all those things get in and out of the Lock, with no effects.
My other theory is the Doctor fell into a parallel timeline after the Time War, which is why his sense of history is all messed up (Long Game, Bad Wolf/Parting, etc).
Sorry it was so long, but I've been thinking about this for a while.