I've not read the entire thread completely, but did anybody else catch the reference to the original series bible and The Five Doctors?
In the original series bible, the Doctor was said to be suffering from the aftereffects of a war. When they started regenerating the Doctor, he was said to relive his past, including the war.
In the Five Doctors, Flavia said, "Once again, it is my honor to inform you that the High Council has used its emergency powers to elect you as Lord President, effective immediately."
It was the Doctor that they decided to send to Skaro to stop the Daleks in the first place, an event RTD has intimated was the start of the Time War.
By the 7th Doctor's era, we were getting hints he was "more than a Time Lord."
Tonight, the Shadow Proclamation's leader said she was confiscating the TARDIS and going to war with the Doctor as their leader. He left them very like the way he left Flavia.
Put them all together, and that's a recipe for a theory that the Doctor's memories of why he left Gallifrey in the beginning aren't completely accurate - that he, in fact, led the Time Lords at some point in the past, perhaps in an earlier Time War - perhaps even a war with the Daleks. No matter how many times he tries to escape it, he can't. In whatever alternate versions of history he exists, he always has to fight the Time War with the Daleks.