Tom's Doctor mentions being blamed for the great fire.Can't remember which episode, might 'Talons of Weng-Chiang.'
My point isthat with it's long history and tons of people involved, mistakes will happen, people like us will notice them, and people on the show will scratch their heads and try and fix them.
The Time War and the Cracks are devices that can be used to fix things, a shorthand. Yes, they could become a crutch for lazy writing, and I do miss the Time Lords, but I like the mystique of the Time War.
and afterall, it's not like RTD was the first to do it, Tom's messing with Dalek history in 'Genesis' has been used to explain away when Dalek history gets timey-whimey.