Braniac and Darkseid are better for the Justice League movie in my opinion. I'd say most likely Lex Luthor would be better for Man of Steel 2. If they want to, they can have Metallo as a henchman. I'd say if you want to think of good villains for Man of Steel 2, it has to go along with the general tone of how Man of Steel is going to play out. Given the tone is set for a gritty, darker and a some-what realistic take on things(while still incorporating the sci-fi, alien aspects) I don't really see villains like Bizarro, Toyman, Parasite or even Mr Mxyzptlk would fit in that world.
I would like to see them do a story line involving the Eradicator. I'd say he would fit right in with all the Kryptonian/Alien sci-fi stuff they've got going on in that world. He would start out as a villain, maybe something Luthor temporarily reprograms from Kryptonian technology salvaged? Then later he becomes good and aids Superman.