Honestly, I don't see why Marvel Studios is the scapegoat for weak villains in superhero movies. Sure, Loki is definitely their strongest villain and most of the other ones can't even compete, but every studio has a few solid villains and a bunch of forgettable to just plain bad ones.
WB/DC: From the Batman movies, both Joker incarnations so far have been their strongest and most memorable villains, with Burton's Catwoman, Nolan's Bane and Two-Face, Ra's al Ghul, and Zod from Superman II rounding out the best of the rest. Hackman's Luthor, Zod (MOS), Scarecrow and Burton's Penguin were above average also. Kevin Spacey's Lex Luthor looked bored out of his mind, but I guess he's the best of the worst. The rest of them are barely worth mentioning at all. Nuclear Man, Riddler, Two-Face (Tommy Lee Jones), Mr. Freeze, Poison Ivy, Bane, Parallax, Hector Hammond? Awful.
Sony: Mainly just the Spider-Man movies here. Doc Ock and Dafoe's Green Goblin were great, but everyone else was kind of lackluster. Sandman, Venom, Lizard, TASM2 Goblin and Electro were all subpar. The less said about Rhino and the lame-ass Ghost Rider villains, the better.
Fox: The X-Men movies have had a few great villains through the franchise, like Magneto (both McKellen and Fassbender), Stryker (Brian Cox), and Shaw. The second-tier villains like Mystique, Deathstrike and Liev Schreiber's Sabretooth were also memorable. Besides them, there's just bad villains all over the place like Juggernaut and the rest of the goon squad from X3, Viper, Stryker (Danny Huston), Weapon XI or whatever the hell Deadpool was at the end of X-Men Origins: Wolverine. Then there's Dr. Doom, cloud Galactus, Bullseye....*shudder*
I'd say that the Batman movies have, overall, had the best luck with villains. But as for superhero films in general, the villains that have worked best on screen are still the most iconic ones, like The Joker.