Ooooooooo, I never like Merging timelines... they never seem to make sense to me in any shape or form.
I know the position of MC is debateable as the first game, but I stand by OoT coming first. They only reason I hear people placing MC first is because Link gets the trademark Green Hat at the end. I havn't even played MC, but looking at my mates copy, it just sems to be implying that Link is the new Hero after such a long break with no Hero.
The quote is:
Also, the state of the Triforce is not accounted for in various places.
And I tend to count Ganondorf's state in games as cannon, such as when he is Ganondorf the Man or Ganon the Pig Demon.