Decided to throw in my choices. I will add some commentary on why at the end.
So, why is BOTW so low you may ask? Or the Minish Cap?
While it had stuff to do; the story felt tacked on and empty.
The combat was also far harder than most Zelda games and had the added downfall of leveling up the enemies as you do; but not actively telling you that it was doing that. This led to several situations where I had to do things the hard way just to get by.
As for the Minish Cap... I hate Ezlo. That's it. Nothing else about the game really bothers me as much as the blabbermouth hat who spouts unskippable hints to do things every Zelda player would already know.
As for my top 3; all of those captured the "explore a huge world and find tons of secrets" feel I want from Zelda.
Skyward Sword was good, but the motion controls were nowhere near as good as those in Twilight Princess.
Plus, I loved the stories for those 3 games more.
In the end, I guess while I like interesting gameplay; I would rather have a good story and a great game to play in.
If there are questions about any of my other choices, please ask.