We could also solve the problem of the third timeline by simply assuming that it came into being when Link first pulled the Master Sword. Alternatively, each pull creates a new timeline, but since they are all identical in terms of plot, only one is relevant in terms of the series chronology.
For the record, we don't actually have to assume that Link died outright; the Hero of Time was never more than a distraction for the Sages to finish their seal, and if Ganondorf stayed long enough in the Sacred Realm after obtaining the Triforce, he might well have remained there until ALttP. We shall see what the official view is soon, though.
The placement of Four Sword Adventures is indeed curious. I suspect it was placed at the end of the child timeline so as to set the stage of more games involving Ganon (and potentially Vaati), if Nintendo would be so inclined.
Vaati's history might be a problem, or not. It is not too farfetched to assume that he could not escape the Four Sword for quite some time, but why FS was not placed immediately before FSA is a mystery to me. His fate is uncertain at the end of The Minish Cap (defeated, but not necessarily dead, as in FSA) and his return to power could have been set at a much later date than this timeline holds. It is worth noting that his origin predates the split in continuity, meaning he could turn up in any timeline if the creators so desired.
