I'm not saying that the villains are amazing I'm saying that acting as if they're utter dogshit is underselling a fair few of them. You'll also realise that many of your examples I didn't mention because, I also agree they're not good. I would never act as if every villain or organisation in those movies are utterly awful because it isn't true.
I agree that the villains are lackluster compared to Batman villains but I'd argue that is because Batman in the Nolan trilogy gets very little development. Hell, I have some serious problems with the way that Batman was portrayed in, especially, The Dark Knight Rises but the villains are usually good, save for Bane who I saw to be wasted potential. Catwoman and Bane in those movies had some great anti-Capitalist/Marxist diatribes about the rich being brought down but that was all thrown out the window just to pull the Talia Al'Ghul twist and what I expected to be a commentary on modern society and excess turned into a basic revenge story. I only say this as a fan of Batman. Point being that the series is largely lauded as being some great example but, aside from The Dark Knight, I disagree.
I agree in that the villains are more interesting but I'd say that it's at the cost of Batman. I'm aware I will probably be hung, drawn and quartered for this.
As for Marvel having better villains at their disposal, maybe, I'm not sure where my position on that is.