While the Joker certainly has his nightmarish qualities, he's such a well-known villain that it almost works against him at this point in comics - nothing Joker does is nearly as terrifying as the above individual.
Due to his actions throughout comic history, we expect the very worst from him. It's the norm.
This is exactly what makes Mr.Bloom more frightening than the Clown Prince, as not only is he a villain created in the New 52, but we have no background to the man behind the mask whatsoever. In fact, it doesn't matter who Mr. Bloom is outside of his Slender Man look-alike costume, because the most uncomfortable part of his character is that he doesn't need a tragic backstory for him to be the way that he is.
There is no chemical vat that made Bloom, and this is what makes him absolutely terrifying. He is developed out of the distrust a post-Year One Gotham has for its fellow occupants, the divides between all of them, and while Batman can beat him up, righting those wrongs is a whole different story.
Batman can beat Mr. Bloom, but he cannot defeat what made him, and the concept of a villain who cannot truly be defeated is the most frightening one imaginable.
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