I think this is a common perception, one I once held until I actually started watching the Superman animated series (WB) and reading more of his comics. Superman has a decent rogues' gallery, it's just that movies and TV shows have relied too heavily on Lex Luthor, excluding the other villains too much. Metallo, Bizarro, Parasite, Brainiac, Doomsday, Eradicator, Darkseid, Mongul, Jax-Ur, General Lane, could all be great movie villains. Even Intergang, Livewire, Toyman, Silver Banshee, Prankster, Mr. Mxyzptlk (with the right approach, like in Whatever Happened to the Man of Tomorrow?), Atlas, Titano, Ultra-Humanite, could all be good secondary challenges, if the new films went the route of multiple villains per film like the Nolan Batfilms have.
Except that a lot of the Superman: The Animated Series
villains were either retooled to make them more effective (like Toyman), invented outright for the show (like Livewire), or borrowed from other comics. Darkseid wasn't really a Superman villain until TAS made him one. And the reason they made him one was because Superman simply didn't have any top-tier archnemeses once you got past Luthor and Brainiac.
I could see Metallo working as the main threat with Luthor controlling him from behind the scenes, like in Metallo's first S:TAS episode. Parasite could maybe work if they used the thing about him gaining people's knowledge, so that he'd learn Superman's identity. You could get an effective psychological-thriller thing out of that; the Parasite could make Clark's life a living hell. Though I'd rather see something bigger like a Brainiac or Darkseid story -- maybe a story featuring Manheim and Intergang with Darkseid revealed as their string-puller and coming into play in the third act.
But Jax-Ur is basically Zod (at least, the version of Zod made famous by the movies and imitated in more recent works is something of an amalgam of the Silver Age Zod and Jax-Ur), and Zod has more name recognition these days so they might as well go with him. And Eradicator might as well be merged with Brainiac, since that's kind of what the S:TAS character already did. Bizarro or Mxy or Toyman would be hard to do without sinking into goofiness and camp.
But not Doomsday, please. Doomsday wasn't a character, just a cheap gimmick. The only times he's been remotely interesting have been in the adaptations where they gave him some personality and intelligence, particularly Smallville