Here's the deal:
We all know that Termina is in an alternate universe to Hyrule and that most everyone in Hyrule had some kind of a counterpart in Termina, yes? The Humans/Hylians had theirs in Clock Town, the Deku Scrubs had theirs in the Southern Swamp, the Gorons had theirs in Snowhead, the Zora had theirs in the Great Bay, and the Gerudo had theirs in the Pirate Fortress.
So that brings up two missing people: the Sheikah and the Kokiri. It is highly supported that Ikana Canyon is the counterpart to Kakariko since both house the dead, both have graveyards, both have music-box related buildings that are connected to the flow of water via the Song of Storms (Windmill Hut and Music Box House), AND both have wells. We know that the Sheikah once inhabited Kakariko and the Ikana (if that was their name), Ikana Canyon, but both are missing. It is obvious that they are counterparts.
Now, let's look at the Kokiri situation. The Deku Scrubs in OoT inhabited the Lost Woods with really no cultural structure, while the Kokiri had their own forest-town. In MM [conversely] the Deku Scrubs have their own cultural structure and the Kokiri? Wild denizens lost to the wilderness in the Woods of Mystery. Remember, the Deku Tree said that the Kokiri would become Skull Kids if they left their forest for the Lost Woods. Well Hyrule was a different type of world. The Woods of Mystery (the obvious counterpart to the Lost Woods) is in a swamp ungoverned by a Deku Tree, so the Kokiri never had a guardian. Instead, they took the feral forms of monkeys. Not devolution, rather adaption. Kokiri are not children, they are forest spirits that take different forms to adapt to their environment. In Twilight Princess, the Deku Tree had already died, but a new tree did not sprout because that only happened in the Adult Timeline. Naturally, the Kokiri would lose their guidance and fall prey to the overgrowing vegetation of the forest, which for a century developed into the Faron Woods. They assume the forms of monkeys just as their counterparts in Termina did at least one hundred years prior to adapt. Again, the Forest Temple in TP HIGHLY resembles the Great Deku Tree's remains, and over one hundred years, it makes sense that much would deteriorate.
And about the Forest Temples in OoT and TP. They are obviously different. The one in OoT is a haunted museum located deep in the woods, while the one in TP, like I said, is the Great Deku Tree's remains.
Hope that clears the issue up.