I played through a few worlds of Super Mario Bros 3 with my GF a few nights ago, the bosses and mini-bosses were excellent. I seem to recall the bosses in Kirby's Dreamland being similarly good, perhaps because the consoles' lack of power prohibited the big wind-up cutscene most bosses have in modern games.
Metroid Prime also had good boss fights, even though it subscribes to the "naught but the weak spot" philosophy the author of the article in the OP hates. But personally I didn't mind them, since you often have enough health and time to figure out how to fight the boss, dodge their attacks and exploit the weak spot. Same with the Legend of Zelda bosses, though I never actually realised how to beat Puppet Gannon in Ocarina of TIme until a few years after beating the game (I slapped him with the Biggoron Sword when he flew near the floor, instead of playing magical tennis with him)
