IMO, I don't think Penguin was ever meant to be a primary villain. More than anything, he's like a cockroach who can't be killed, mostly hiding in the walls, but we'll see him scurry across the floor from time to time. He only had "five or six" scenes in the first movie, so that sounds about right for the second movie as well. Maybe in the third movie he'll have a bit more to do, or at least one, last memorable showdown with Batman. And probably another season of TV just before that, it sounds like.
As for the true villain for Part II, it's looking more and more like the Court of Owls, and then one of either Hush, Clayface, or maybe even Mr. Freeze. Those seem to be the leading rumored candidates as of now. Then, of course, there's talk of limited appearances from Riddler and Joker again (with Joker all but confirmed to be the main villain in the third movie). In other words, there's no shortage of potential there, and Batman will more than have his hands full in that regard.