Re: Did anyone else NOT view the Time Lords as the "bad guys"? SPOILER
I think the Timelords are a people who have been at the top of the tree for a long time, had a superior culture and technology longer than most anyone else, and as such have all the arrogance that goes along with that. Their final solution to the Time War was extreme yes, but how enlightened a society would you have to be to actively allow yourselve to die out to save the universe?
The episodes really did cover this stuff, look at the end of Waters Of Mars.
Exactly - this entire issue is in fact the "arc" of the Specials season -the arrogance of the Time Lord.
In "The Next Doctor," 10 is faced with a man who desperately wants to
be the Doctor because to be the Doctor is such a wonderful thing, and who gets the whole of London cheering that the Doctor is a hero and a saviour. This boosts 10's ego after a breakdown in "Journey's End."
In "Planet of the Dead," there's another fanboy telling him "you're bloody fantastic, you are." The story ends with 10 first of all sticking to the rules by turning Christina over to the police. But then changes his mind and decides he's above the law, and uses his power to set her free with a new toy she absolutely should not have.
"The Waters of Mars" is completely about this - the dichotomy between knowing he has to power to change things, and knowing that he shouldn't. He finally decides he's above all the rules of time and space, that those rules don't apply to him, and that he can do whatever the hell he wants, regardless of the effects on "the little people" (who really ought to be grateful for his help, shouldn't they?) because there's no-one with the power to stop him.
And finally in "The End of Time," we get the ultimate end-point of that mindset. The Time Lords consider themselves above the rules because, as you say, they've been at the top of the tree for so long and no-one can tell them "no." And confronted with a whole planet's-worth of arrogant Time Lords, he realizes that he's become as bad as they were, and he has to stop both them, and himself.