I don't know, I think it's only been recently with the advent of the Marvel Universe that many of the villains seem paper-thin. Previously in many of the stand-alone movies, before the idea of a Marvel or DC Universe, the villains were fairly decent. Below are the villains I think were much more than paper thin. My only problem was with Heath Ledger's Joker who, was such a great character, he completely overshadowed Christian Bale's Batman, in my opinion.
Superman II - Zod
Batman - The Joker (Jack Nicholson)
Batman Returns - Catwoman
X-Men - Magneto
Spider-Man 2 - Doc Ock
X-Men 2 - Col. Stryker
The Dark Knight - The Joker (Heath Ledger)
Since then the only really great villain, most people agree on, is Loki. Other than that, the villains really aren't that interesting. Zod wasn't bad and I think the Red Skull was better than most people think but we really aren't given much meat about a villain. I actually thought ASM 2's Green Goblin was probably the best villain of ASM or ASM 2 and was way better than Electro.
The Marvel Universe really does lack villains these days with truly good stories and depth.