Lets see:
Mechanised transport - Nope. We've already had trains.
Jumping - Nope. Zelda 2 and Roc's Feather exist.
Multiple smaller towns to visit - Nope. It's the same as Zelda 2.
Open overworld - Nope. Zelda 1 and 2 had this. Sure both are not as nonlinear as BotW but the world was mostly open from the start.
Rafts - Nope. Zelda 1 and Zelda 2 had them, as well as other Zelda games.
Stamina meter - Nope. Skyward Sword exists
Only 4 main dungeons before the end game area - Nope. Majora's Mask also had this.
Pulling the sword from the stone - Nope. That's in many Zelda games.
Side quests - Nope. They exist in many other Zelda games. Majora's Mask featured them heavily.
Sense of exploration - Nope. Zelda 1 had this. For 1986 Zelda 1 was a masterpiece of overworld exploration. BotW is similar just beefed up to 2017 standards.
Hundreds of little collectable things (seeds) - Nope. Skulltulas, kinstones and other things exist.
Shrines - Nope. Zelda games have had little underground grottos in the past where you had a little challenge to get a reward. BotW just formalised the process and gave them a name - Shrines.
Most of the heart pieces earned outside dungeons - Nope. Majoras Mask was also like this.
Breakable weapons - Nope. Ocarina of Time and Majora's Mask had this. Possibly other Zelda games too? BotW did massively expand on the idea and made it a core feature of the game but it's not a first for the Zelda IP.
Voice acting - Nope. Zelda CDi. Of cause the CDi games are not made by Nintendo and they are hot garbage but they did have voice acting.
Horse travel - Nope. Epona exists.
Cooking - See edit 2 below.
So what is actually new?
I don't know to be honest.
[edit] There's a new physics engine. Is that a new feature? Well I guess many of the 3D Zelda games had new physics engines but BotW's one was quite different and new so I guess it applies too as something new to BotW.
[edit 2]
If we're going to call the Giant's Knife and razor "a breakable weapon mechanic", we're going to have to call a spade a spade and admit that Wind Waker had grandma's soup, Link's Awakening had a pineapple being cooked, Skyward Sword had pumpkin soup...lot of soup.
So it looks like cooking is off the table as well. It's not Link specifically cooking himself but the idea has been previously used and expanded on in Breath of the Wild. I've edited my above post to reflect this.