The problem, Jack, is that the characters you're listing AREN'T one-dimensional, unless you take only the most superficial looks at them.
Red Skull is an evil genius and a master strategist, capable of creating intricate, long-running plots and influencing and subverting those around him to serve his own ends. None of that except 'evil' could be used to describe Clockwork. Further more, the Red Skull has, throughout his run, been the puppetmaster and man behind the curtain, often manipulating heroes to fight their friends and using a wide array of poisons, drugs, and devices.
The only one of those villains you mentioned that comes close to being one-dimensional is the Joker, and that is because the Joker is, in a word, insane. He is a force of chaos that you never know what he'll be up to next, always coming up with some new joke to play as he obsesses over Batman. And the most powerful Joker story ever? The Killing Joke, where they go into depth with Joker and his backstory, fleshing him out and making him less one-dimensional.