I love this game and all, but the story makes no sense. As far as which link this is, I think its yet another seperate reincarnation. Link had to fight calamity ganon, which none of the other links did. You could say a different link beat ganon in his game, then had to fight him again pre botw as calamity ganon, but that wouldnt explain how it / he got free again... In fact... The game doesnt touch on this at all.
Spoilers ahead!!!
Now. The end of the game. After you beat calamity ganon and he goes all beast pig on you, Zelda tells you that he has given up on reincarnation in a desperate attempt to win.... Ok.... So why did they seal him away at the end and not kill him for good? How does he come back in future games in the timeline if he cant reincarnate any more, and why would every game that takes place after this not have calamity ganon instead of whatever is actually in it?
Next we have the technology. According to the game, the ancient shieka made it all... Ummm.... When? We know tech of this level has existed since at least skyward sword, but it is CLEARLY lost in future games. So when did the shieka make the guardians? Where did they go after botw? Why is it different tech than what we see in skward sword? Considering how the tech was lost to people and they had no records of it or any idea how to use it, we can assume that happened WAAAAY before the 100 years included in botw's story. So where does this all fit in? In my head.... nowhere.
I love this game, but I really felt it was more skyrim and less zelda. The story made no sense, the dungeons were short and boring, plus the new terminal gimmick was dumb imo. I like the old style of dungeon better. The game barely has any enemies you'd normally expect from a zelda title.... I could go on. This game was a huge stepping stone for Nintendo to take their IP into more modern style game, but it still needs work. I'm looking forward to the next one!