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To prevent the Time War from tearing the universe apart, it is also stated by the Doctor that the Time Lords themselves had become nearly as bad as the Daleks.
This was explained in "The End of Time" (Part 2). Briefly, the Time Lords, led by Rassilon, intended to bring an end to Time itself (destroying the universe) and to "ascend" to become beings of "pure consciousness", free of the constraints of cause and effect. Because that would have wiped out absolutely every other lifeform -- and everything else -- the Doctor stopped them.
In "The Fires of Pompeii", the Doctor had to make a "terrible choice" (Caecilia Evelina's words): If he stopped the Pyroviles' plan, Vesuvius would erupt, destroying Pompeii and everyone in it. If he didn't, the Pyroviles would convert the entire planet into a habitat suitable for them but lethal to humans. As the Doctor himself put it, "It's Pompeii or the world." At the end of the Time War, he had an analogous choice on a far larger scale: It was Gallifrey or the universe.
In "The End of Time", on the Vinvocci ship, the Doctor was talking to Wilfred Mott (who had encountered the Daleks) and said, "You've seen my enemies, Wilf. Well, the Time Lords are more dangerous than any of them." the Doctor didn't think the Time Lords had become nearly as bad as the Daleks; he thought they'd become worse.