Main villains:
Spider-Man: Green Goblin(main villain)
Spider-Man 2: Doc Ock(main villain)
Spider-Man 3: Sandman(main villain), Venom, New Goblin
The Amazing Spider-Man: Lizard(main villain)
The Amazing Spider-Man 2: Electro(main villain), Rhino
Spider-Man main villains origins are based in scientific accidents:
Green Goblin(main villain) - Good guy, Serum makes him crazy.
Doc Ock(main villain) - Good guy, accident makes him crazy
Sandman(main villain) - Sad story, accident makes him Sandman
Lizard(main villain) - Good guy, serium makes him crazy
Electro(main villain) - Good guy, accident makes him Electro
Even Eddie got his powers by in the right place at the right time. Even Eddie played a good guy, just a little bit selfish.
Only villain who is not created by accident is New Goblin, but he is not main villain, and end of the movie, he is a good guy.
Spider-Man main villain has at least 3 action scene against Spider-Man.
Green Goblin(Party attack, burning house, bridge)
Doc Ock(bank, train, old house)
Sandman(bank car, subway,construction site)
Lizard(sewers, high school, oscorp tower)
Spider-Man main villains are sympathetic.
Norman Osborn is good guy, and by accident he turns to bad guy
Doc Ock is good guy, and by accident he turns to bad guy
Sandman is good guy, and by accident he turns to Sandman
Dr. Connors is good guy, and by accident he turns to Lizard
Max is good guy, and after accident he turns to Electro
Coincidences:
In the first (Raimi) Spider-man, Peter Parker turns into a Superhero. And the Supervillain he has to fight just happens to be his best friend's father.
In the second Spiderman, he has to fight The Octopus, who just so happens to be the scientist that Peter Parker has taken on as a mentor.
In the third movie, he has to fight the Sandman, who just so happens to be the guy who really killed Uncle Ben. He also has to deal with Venom, who is really Peter's rival at the newspaper (although this one isn't entirely coincidence as Brock was turned into Venom while following Spiderman). It is a pretty big coincidence that the alien material was found by the one person who already has superpowers.
Then the new movie, The Amazing Spiderman comes out and it has the exact same insanely improbably coincidences. Spiderman has to fight the Lizard, who just happens to be the scientist he tracked down because he worked with his father
And the girl he likes just happens to be the daughter of the chief of police who just happens to be leading the hunt to track down Spiderman.
Can you find those things in Iron Man, Thor, Captain America, or in Batman movies? NO!

In short:
1. Main villains origins are based in scientific accidents(All Spider-Man movies, other movie villains are coming from somewhere else)
2. Main villain has at least 3 action scene against superhero(Thor, Iron man movies, captain america, hulk has always 1 or max 2 fight)
3. Spider-Man main villains are sympathetic. Loki? He was greedy from start.
4. Coincidences, every villain is connected to superhero. Only possible in Spider-Man movies.
Spider-Man movies have something that no other superhero movies has.
Good or bad thing? I don´t know, but other superhero movies has only 1 villain fight scene, while in Spider-Man movies it´s always 3 at least.
This shows how different Spider-Man is.