Pasternak from Ace Combat 6. He himself is a pushover, but if you're going for S-Rank, you have to shoot down 25-30 of these little drones flying everywhere... It's a tedious, frustrating nightmare.
Come to think of it, the mission where you're flying in the mountains and have to shoot down the drones flying recon for the Aigaion is even worse, since you have to fight those drones. The whole mission is a low point in the game.
That's the most recent one I can think of, but being longtime RPG player, there are tons and tons of bosses in old-school RPGs that are just awful, awful, awful. Back in the day, when it was cool to be Square, developers were totally OK with sending the player to the game over screen a dozen times if it meant getting the message through that that boss is a badass.