Most recently, Shadow Mitsuo from Persona 4 was immensely annoying. He not only has attacks capable of having your party's HP, but can hit the weakness and KO one character at a time before you have a chance to react. He isn't the worst boss, but his HP is high enough to make the fight about 45 minutes long. This is mainly because he literally creates another boss as a shell... which you have to beat up around three times.
That was satisfying to be done with.
That was satisfying to be done with.