(Here's the final 3, they're actually quite surprising! I bet you didn't see any of these coming! )
3. Kalle Demos
Though the boss battle strategy is very similar to battling Barinade, it's so much more thrilling.
What game has there been where the boss battle is actually beautiful? Usually when you get to the point of the battle where you get critical damage you might get a swollen eye in your face or a tired body, but not with this. You get a beautiful flower. The entire room changes from the light of this flower.
Barinade and Morpha both made sense with the disruption they caused and with the temples they were in, but Kalle Demos makes any more sense.
It's a plant causing other plants to die and ruining the lives of tree spirits. It fits together so well. I feel like I've heard of this happening several times. You shouldn't plant certain plants in places because they will kill the other plants around them.
This boss is also a perfect example of not judging a book by it's cover. It looks like a beautiful flower, but it's actually a deadly boss!
It fits the magical feeling of Zelda and is by far the best plant-related boss in the entire series.