I wanted to try doing animated style designs emphasizing that prominence of green/secondary colors on Spider-man's villains, actually. His most dangerous, antagonistic villains would emphasize the green and purple, cool colors;Green Goblin, Mysterio, Vulture,Beetle, etc. Villains with some more humanity or with some tie to Peter would be primarily green with orange played up as a secondary color; Doctor Octopus with orange gloves, boots, and harness for the tentacles, Lizard with orange eyes,and a yellow orange underbelly, Electro. Villaisn with more personal motives would be warmer colors, mainly oranges and reds, Shocker, Kraven, Hobgoblin. Rhino's grey would be purple tinged.
For characters like Venom, or Kingpin, who don't fall under those broad strokes, their tones would be shades of colors(for example, the shading to Kingpin's white suit would be purple, along with purple pants and green tinged white undershirt with orange vest). Venom would be initially purple toned, but turn blue when he becomes more of an ally. Carnage would be the most divisive since his red would be toned orange which probably wouldn't fit him individually but would work with the others in collaboration. Allies like Black cat or Morbiusn would use blue tones.