Im going to look at the Master Sword and its 5 biggest titles, WW,OoT, ALttP, SS and TP. Its simple to tell that it was made in Skyward Sword, however if you look at OoT you'll see it wasnt "blessed" (The light that shines around it in TP and WW near the end of both games) this leads me to think that the Twilight Invasion resulted in the final form of the Master Sword in WW. Same with where it was found in each game. If we assume that Gannon succeded in OoT (the "Dead" timeline) A Link to the Past suddenly makes shit loads of sense. The Master Sword being found in the Sacred Grove leads me to think someone (say a preist or even Shiek or Impa) hid it there as sort of a emergency location. Link then finds it there as intended in A Link to the Past. Gannon ruling the Sacred World makes sense if the first hero fails, the Maidens (assumably the desendents of the Sages) managed to protect Hyrule from Gannons direct influence, till they are all captured by Agnm (I forgot how to spell it
) and dumped in the Dark World (Sacred World under Gannons rule). Also, I think people have TP all wrong. I think TP was BEFORE, OoT.
Think about it, the earliest game we see the Temple of Time is OoT right? WRONG! Its SS! Leading me to believe that the Master Sword was kept in the Grove till some time after TP. Then it was kept in a NEW Temple of Time (in fact, I think the Forest Temple in was the same old Temple of Time we see in TP, which I think was SS temple. In other words, I think the Door of Time was moved serveral times in its history. Which explain why the Temple of Time in TP is a reflection of the past, yet there is no Temple of Time in the Castle Town, it was some sort of Temple in between SS and TP. Ofcourse, that whole TP before OoT theory can be ruined by asumming that Castle Town was moved after the events of the Adult timeline in OoT, it would explain also why the entire area seems strange, yet also familiar. Half if that map could be the Hyrule we know from OoT, and half of it could be the new areas claimed by Hyrule since thier capitial was moved.
Wow, I just read over this and it has quite a few holes that im too lazy to fix. Feel free to widen them so I can properly correct myself