if you think about it though, the only reason most bosses in 3D zelda games are so easy, is mainly due to the pace of the battle! Take Gohma for example. i only choose this cuz EVERYONE has fought this battle! This is a Super Easy battle, but lets just say we speed her movement up, and give her some projectiles while she hiding up on the ceiling, add in the eggs she drops, and make her more aggressive while the underlings are attacking, and you might have a pretty tough battle.
It all has to do with the pace. I feel one boss that could have been a pain in the butt if not so slow is Koloktos. Epic battle, you can watch you tube videos that make this battle look easy as hell, but its not as easy as they make it look. I remember being Very frustrated with that battle even at the slow pace, it came to the point where i make Koloktos take out all the pillars so i could refill my hearts. However if you speed the battle up, and add nothing, that would be and extremely difficult boss!