Green Lantern, Lex Luthor, and the Joker are no-brainers.
The "return" of Deathstroke and Captain Marvel (or "Shazam", as he's now called) would be nice. Particularly the latter.
I'd like some of the Titans to show up. Raven, Starfire... Cyborg would be good for the "gizmo" side... and Beast Boy would certainly feel unique. I'd suggest Robin or Nightwing, but between Batman himself, Harley Quinn, the Joker, and possibly Solomon Grundy (I forget his original source), I'm concerned about overloading it with a Batman cast.
Would love to see some powerful Big Bads like Deathseid and Brainiac... but they MUST be playable!
I'm not holding my breath, but Blue Beetle would be awesome to have, particularly the Jaime Reyes incarnation, but I'd happily take Ted Kord if it meant Booster Gold was included.
Aside from all those... Black Adam, Sinestro, and Green Arrow. Only real concern with the last is that his range focus seems a bit ill-suited for such a melee-focused game.