Playing through, one thing that has bothered me is that it isn't really steeped in the old Hyrule mythos. I haven't made it to the end yet, so I may be missing a great deal, but the three Goddesses, the Triforce, Ganon, a lot of other things (the way bombs work, the clockwork beetle instead of a boomerang, many many other things) just seem so unlike any of the previous games that it honestly feels like it was a completely different game with Link added in as an afterthought. This kind of makes me sad twice: first because it means there was potentially an entirely new franchise they could have started building upon; second because it is a very un-Zelda like Zelda game that they now have to shoehorn into the timeline they are so keen to try (and fail) to make work.
edit: that's not to say I'm not enjoying it and don't think it is a fun game, there's just so many things that strike me as "not-Zelda" that I feel it would have been better served as an original content game than trying to be a Zelda game.