Well, the big holes in Earth-38 Superman's rogue's gallery are Brainiac and Darkseid. Neither of them have been established as villains he's faced already (though Brainiac 5 from the future has mentioned him facing his ancestor at some point), so either one could be season-long Big Bads. This Supes also has an established history with Mongul and spent some time on Warworld, so maybe Mongul/Warworld comes to him this time for another Big Bad threat.
Aside from them (and of course Lex), I'm actually looking forward to seeing a lot of the smaller villains that would never have a shot in the movies: Atomic Skull, Ultra-Humanite, Eradicator, Titano, Imperiex, Mr. Mxyzptlk (who's already appeared on SG but could of course take a different form with Supes), Vyndktvx, Kryptonite Man, Hellgrammite, Intergang, Equus (actually, while I'm against adapting "For Tomorrow" as a movie, the basic concept of it could make for a GREAT storyline for this show in one of the later seasons now that I think about it)...he's got a really fun and diverse rogues gallery that movies never even get to scratch the surface of.