I think you can incorporate Freeze into the "power grab" angle. Penguin is competing with other mobsters for control of Gotham's organized crime circuit, and there's some guy running around robbing his banks. He assumes it's some other crime boss trying to weaken his position (Maroni, Ventriloquist, Thorne, take your pick), and it only stokes the flames of "war" even higher. Of course, Freeze robbing these banks has nothing to do with Penguin specifically but rather to fund his research for his wife. Or instead of robbing banks, Freeze is targeting GothCorp and Penguin owns a controlled stake in that company. Again, he thinks it's another crime boss trying to sabotage his business efforts. In the third act, Penguin finally figures out who the guy is that's screwing with his business and he sends his men after Freeze. The final action sequence: Penguin and his goons vs Batman and Freeze.
I know we have the Penguin spinoff coming, but I don't see how the first film could end with such a strong emphasis on a bloody power grab and then Reeves doesn't address it in the sequel. So whether it's a mob war, or the freaks of Gotham coming out to play, you can't dangle that plot point and then never circle back to it. So whichever villain Reeves chooses as the main antagonist (or antagonists), I have to think it ties into that.