Focusing only on the villain. I'll compare Khan and his actions and motivations to the comparable villains of the other Trek films. They being First Contact, Nemesis and XI
Torture: Checov, Captain Terrel with mind worms and 5 scientists on Regula
Kill Civilians: 5 Regula scientists
Kill good guys: Crew on board Enterprise, Spock dies in battle
Attacks Targets: Disables and nearly cripples the Enterprise when he attacks it while ENT's shields are down.
Motivation: Get revenge on Kirk for stranding him on Ceti Alpha V, loss of his wife, and Acquire Genesis device for unknown purposes.
Succeeds at: Acquiring Genesis
Dies: During climax of the film after being beaten by Kirk in a tactically neutral area
This is everything Khan does in TWOK. Using this format I'll compare to other villains who carried out similar actions.
Torture: Crew members of ENT-E by taking away their individuality and humanity and turning them into zombified Borg Drones
Kill Civilians: Member's of Cochrane's team on the Phoenix project
Kill good guys: Crew on board Enterprise, crew aboard other Starfleet ships during the attack on Earth.
Attacks Targets: Earth in the present, and Earth in the past.
Motivation: Add Earth's biological and technological distinctiveness to their own.
Succeeds at: Conquering Earth in the past and assimilating the planet.
Dies: During climax of the film after the Phoenix's history is secured and Data breaks the warp funnel.
Torture: Troi with mind rape and Picard with character assassination of how he is Picard and all the horrible acts he plans to commit.
Kill Civilians: Romulan Senate
Kill good guys: Crew on board Enterprise, Romulans in Valdore ships
Attacks Targets: Disabled 2 Valdore Romulan ships, attacked Enterprise causing massive damage.
Motivation: Erase Picard from history and destroy everything Picard stood for. Prove that the clone is superior to the original "echo triumph over the voice".
Succeeds at: Staging a coup d'etat and allying himself with Romulan Fleet for an attack on Earth. appoints himself Praetor of Romulan Star Empire.
Dies: During climax of the film at the hands of Picard, after Picard had disabled Shinzon's ship's weapon and cloaking abilites.
Torture: Pike with throat slugs
Kill Civilians: Crewman aboard Kelvin, and entire planet of Vulcan and billions of it's inhabitants
Kill good guys: Crew on board Enterprise, Kelvin, entire crew of 5 Star Fleet ships arriving to assist Vulcan
Attacks Targets: Attacked 7 Federation ships, destroying 6 of them. Destroyed 47 Klingon War Birds, and Vulcan the planet.
Motivation: Revenge against Spock in both realities for allowing Romulus to be destroyed and his wife and child dying. Destroy Federation he also holds responsible for the loss of Romulus
Succeeds at: Acquiring Red Matter and destroying Vulcan
Dies: During climax of the film at the hands of Kirk and Spock after they crash red matter into his ship.
Dare to compare. By comparison to these other villains, Khan's lists of accomplishments aren't as staggering. In TWOK we are told and reminded constantly of Khan's high intelligence but none of his actions really display that. He's comparable to Nero in the sense that he merely got lucky having a ship he could maneuver around the galaxy with. Neither one of their actions or victories display any ingenuity on their parts. I think fans of the movie project the villain Khan should be over the villain he actually is. Khan SHOULD be a genetically enhanced super-man with a genius mind, amazing strength, sense and reflexes, with an equally large ambition and a string of victories to his name. What Khan IS, is a villain who got lucky in acquiring a Starship and only tangible victory was crippling the Enterprise because Kirk didn't see the danger from a friendly vessel. Which resulted in Kirk dropping Reliant's shields and firing back at Khan. Kirk's use of the prefix code was ingenuitive.