The hardest boss I've faced would have to be Boost Guardian in Metroid Prime 2. The fight seemed to be more about luck than anything and he never seemed to destroy the towers for health when I needed him too. I got thrashed by him a boatload of times but what was weird was that when I finally beat him, I didn't lose much health. Even when you know what to do, it's still hard
Was he harder in the original version or something? I have Metroid Prime Trilogy, and I kicked his ass without even losing a bar of health.