Metroid Prime in......Metroid Prime.
The fight with Prime was fine. But then you have to fight the Prime Core, which is just annoying. It's one of those bosses where you are given a super-mega weapon to damage the boss. That alone is disappointing and annoying. The boss also has pretty much one attack; an incredibly slow wave-of-doom that can be avoided by......jumping. Talk about lame. You also have to keep switching your visors during the fight, which is also pointless and annoying. Also, the Core spawns metroids. A boss spawning enemies is annoying in general, but when these enemies can latch on to you and prevent you from doing anything (like jumping to avoid the stupid doom wave), it takes the frustration to a whole new level.