Draygon is the right answer.
This is a thing?!! Brb replaying Super Metroid.
It took me the longest time to learn that wasn't the only way to beat Draygon. After I figured it out on the first pass, it never occurred to me to approach the fight straight-up. (Similar experience with the Imprisoned in Skyward Sword, where I jumped on the head, a friend of mine stabbed the toes, and it never occurred to either of us that the other's method worked until we compared notes. Not nearly as good a fight or pleasurable a solution as Draygon, of course, and not even in the same league as the best fight in Skyward Sword, Koloktos. Lopping off the enemy's limbs and turning its weapons against it? Sign me up.)
As far as alternate methods for killing bosses go, several of the hard-mode achievements in World of Warcraft's best raid, Ulduar, surely qualify. The best of these, Mimiron, began with pushing a conspicuous red button that set the room afire and forced all the players to stay on their toes throughout the whole encounter. Back when the raid was current and couldn't be blown through with superior gear, achievement runs imposed all kinds of demands on coordination and positioning that necessitated a thorough understanding of all the boss mechanics. This is true of high-end raiding generally, but it was in achievement runs like Glory of the Ulduar Raider where you could really draw out a whole variety of mechanics just by approaching the fights differently, something that hasn't been the same since now that WoW raids have strictly delineated difficulty settings separated by stats instead of raw encounter design alone.