Jumping back in with a reply to earlier posts:
What also intrigues me is how the temples throughout the different games link to each other. The most remarkable one is the Temple of Time. Keeping only in mind the one thingy that links them all, The Master Sword, the temple of Time in Ocarina of Time seems closest to Hyrule Castle in WW, whereas Sealed/Hylia's Temple compares better to Twilight Princess' Temple of Time and a Link to the Past's Pedestal of Time. Some theories speculate on how the Master Sword was moved throughout the ages, but that seems somewhat farfetched in my oppinion.
What I am inclined to believe, however, is Lanayru Temple of Time -> Spirit Temple -> Arbiter's Grounds. Not only to the ST and AG both feature the Sand Goddess (?) with the Snake, AG and LTOT both feature a mirror-like portal to a different realm (time/space) and the ST forces you to travel through time to complete it (that and the mirror shield /shot'd). It's also not hard to believe that criminals were judged in the temples of the desert. With the tumultous history of Lanayru of war and what not... you could also think that the Gerudo (and their ancestors) weren't kind with intruders and sent them to be judged before the Sand Goddess. As a final, there's the Arbiter's Grounds where criminals were judged (see Ganondorf, right there, though that was OoT in TP |D). I don't know what to make of the Arbiter's grounds... it's got a mix of a prison, a place of death (redeads/poes) and a sacred place.
My guess about the Shadow Temple is that it's more of a mausoleum/prison than an actual temple (or that the temple/place of prayer is restricted to the first room with all the torches). We shouldn't forget that the Shadow Temple is directly linked to Hyrule's Bloody History of War.... War is a horrible time... so it's not hard to imagine that the Shadow Temple and the Well were used for horrible things. BT
Big Tree (SS) - > Great Deku Tree (OoT) -> Forest Temple (TP)? 8D;
I'm not a fan of the 3-split timeline either.... that's my biggest concern about the offical timeline. I don't like the idea that there's a probable time line. It creates the thought that those games could have never happened. And though I support the idea that a hero might fail, I don't think OoT Link is the one that should bear the responsability for the triple split. Maybe the Link before him, but not OoT Link... OoT Link doesn't fail.
And Japanese Username's username reads as Konankun. ;3