I always thought he was a pretty difficult boss. Its been a while since I played OoT, or more specifically fought that boss in the game, but I do remember there being problems with me being able to shoot him in the eye. And also with him hitting the floor and making me bounce up and down caused some trouble with it as well. Considering the pretty simple difficulty of every other boss in the game, I believe Bongo Bongo is one of the more difficult ones. He's not fun/difficult like Twinrova, just more aggravating/difficult.