Brainiac-He's the biggest Superman villain that hasn't been done yet.
Metallo-I've just always like the idea of his character. Plus Superman+Terminator=awesome.
Parasite-Another villain that Superman can't just punch, cool.
Darkseid-Although I consider him more of a DCU villain. So he should probably be the villain of a JL movie.
Maxima-We need more female villains and as others have already said, she's not entirely evil. It makes for an interesting dynamic.
Livewire-A good "henchmen" villainess, perhaps working for Lex.
Doomsday-They'd probably need to tweek him so that he has at least SOME kind of personality of his own.
General Sam Lane-An antagonist who has the power and authority of the government/military on his side. Plus it'd give Lois more character moments.