One of the things I found interesting that RTD established as the conceit for the story is the concept of lateness for a time traveler. He repeats this a number of times in the commentary. Logically, it is really strange idea and it's sort of inconsistent with what he's already presented and even what he continues to present in the finale especially in regards to Gallifrey and the Time Lords. This post is just me trying to pull my thoughts together in an attempt to find something coherent... but I won't be surprised if it just continues to be one big mess.
Full disclosure: although I do have a huge tolerance in my willing suspension of disbelief, really huge logical inconsistencies make my brain hurt and ultimately they lead to dissatisfaction for me. I hope that Part 2 will bring it all together so that I won't be left feeling dissatisfied. Fingers crossed.
At the end of S1, Rose realizes that although the Doctor is fighting the Daleks in her future, it's also happening right now as she struggles to think of a way to get back. I get the impression that a not-insignificant length of time is happening in Rose's timeline as she thinks of how to get back to the Doctor while the Doctor experiences it in only a few minutes. To me, that means that time is working like Back to the Future: all of time exists like a book with every page already written, but people can jump to any time period and alter the text of the book. Changes in the timeline affect all of the other bits immediately, except for the items that are "fixed points in time" and cannot be changed (although the Doctor demonstrates that they CAN change them to some degree as he did with "The Waters of Mars"). I'm down with that concept.
I can accept that the Doctor has a difficult time controling exactly when he manages to dematerialize the TARDIS, which is one way that he can make himself "late" for an event even though he is a time traveler. The act of jumping to a point in time and dematerializing establishes a point in the book of time that he does this action and, thus, because he can't cross his own timeline (except for cheap parlor tricks) by leaving and showing up earlier. No logical inconsistency there.
Paradoxes can exist, although they are problematic and require a great deal of energy to keep them up, as the Master used the TARDIS to keep the paradox possible at the end of S3 (although I didn't believe the situation reached a genuinely extreme paradox state (ok, that statement is really weird to make, since situations are either a paradox or they aren't, right? Yeah, this is a jumbled mess of thoughts). If any humans still exist, the human race can still theoretically come into existence again through a single common ancestor).
We also know that there are parallel universes, alternative books of time. Rose and her family is in one of these parallel universes. Jumping from one universe to another does not create a paradox, even though seemingly paradoxical situations could exist from one's perspective (Mickey's grandmother died in our universe but still lives in another). The difficulty jumping from one universe to another seems to be inconsistent. In "Rise of the Cybermen", it seems to be something that can happen accidentally and when done deliberately, it's really difficult and they can't go back as the rift in time needs to be repaired. However, it seems that Torchwood manages to develop/steal technology that doesn't require the entire energy of the planet in order to open up this rift in "Army of Ghosts" (and alternative!Torchwood has portable devices that allows jumping from one universe to another provided a rift is open). Then, just to communicate, the Doctor destroys a star in "Doomsday". Hmm.
Time travelers need a context in order to have discussions. Captain Jack is from the future, a future where he was a part of the Time Agency. When he encounters Captain John Hart, we learn that the Time Agency has shut down. I presume that this is in Jack and John's shared timeline that exists parallel to their own lives if they lived in the 51st century. So, even if the Time Agency is an organization that doesn't exist yet and won't exist after a period of time, there is an established period that they do and other than rogue members like Harkness and Hart, the Time Agency's existence is finite.
It looks like the set-up for the Time Lords is that it is "the last days for their existence", as Gallifrey looks like it is war-torn. In the scene that the Time Lords are talking to each other, they seem to be talking about the Doctor in their present/the Tenth Doctor's past. He's disappeared, but he "possesses the moment". I wonder what that means. The dialogue is interesting. "This is only the furthest edge of the Time War... with time itself resurrecting them, to find new ways of dying over and over again." Are they stuck in some sort of time loop or distortion? If Time Lords exist "out of time", then they only have a time context with themselves and not in the timelines that we enhabit?
When the President is talking in other contexts and is doing his narration, it seems that he is talking about the Doctor as he is encountering the Master on Earth, which is set at a different time period along the Doctor's timeline from the Doctor that is existing with the Time Lords at the same time as the end of the Time War . This is where I'm having a hard time figuring out how it all fits together.
The Doctor mentions in the trailer that "the Time Lords are returning". How will the Time Lords by-pass their own destruction? It's an event that they share along with the Doctor (in the Doctor's past, even if it has a context outside our book of time). I can see pockets of Time Lords being able to escape destruction here and there, but how will they completely negate an event shared by one that does exist past that event? Perhaps with a massive reset may come to pass, but exactly how satisfying would that be? (Especially since we've seen it before, so I've refused to consider this one of the potential options as the resolution for "The End of Time".)
I don't believe there will be a reset. I get the impression that there will be some massive sacrifice and that sacrifice will be what "powers" the paradox of the Time Lords returning, so that the Doctor's actions during the Time War can be ignored... while still being able to end the Time War to the extent that it has been ended. Exactly the nature of it, I feel I don't have enough information yet to know. It's Sunday morning and I really should have breakfast, but I wanted to write some thoughts down before Part 2 comes around and it'll be a bit late to jot them down. Hee!