Oh man, I disagree on the final boss. I thought it was probably the coolest Ganon/dorf fight we've had in the series. I mean, atmospherically they always do a great job with him, but gameplay-wise this was the most complete fight with him we've ever had, he used almost all of his major tricks from across nearly forty years of games and many of the Ganondorf leitmotifs from over the years made an appearance too. Usually with Ganon and his phantoms we either get magic volleyball or a pure melee fight, but this time both his status as a warrior and a sorceror are really on display. He uses four different weapon types, he's shooting demon magic in the more classic Agahnim-style and as arrows, he's creating gloom shockwaves, conjuring phantoms, he can perfect dodge. Again, from an atmosphere standpoint I pretty much like every Ganondorf fight, but gameplay-wise I think this is like a distillation of everything he is as a boss. Plus there's great moments where the gameplay converges with the story in ways it rarely has before, like that moment where his health bar goes past the usual range or having the Sages actually fight alongside you, instead of just "lending their power" in a more vague way like they have in previous games.
I agree about it being one of the best games of all time, though.