You can see my timeline in my sig, but essentially I've placed the "Vaati Trilogy" on it's own separate timeline. Basically out of necessity and lack of clear connection with the rest of the games. You can basically think of the Vaati timeline as a parallel universe with all the same people (Picori/Minish and Ganondorf still exist in both), but the course of events is different. In the main timeline, we never see the rise of Vaati (or haven't seen his rise yet), which could mean a million different things....maybe Ezlo caught onto his "evilness" early on and never trained him, or maybe Vaati simply got eaten by a cat one day while he was randomly hiking in the woods...who knows.