You'd get to take turns across the city, as every story weaves a bigger web, with a healthy dose of playable villains: Harley as the master-criminal-on-the-edge, aided closely by the likes of Ivy, with a sprinkle of the "very" dynamic Two-Face & Penguin duo, and a few pinches of Riddler (sans-trophies), Mr. Freeze, and some other long-awaited obscurities further explored. Icing on the cake; wouldn't it be great to even get a little nod to the beginnings of the Suicide Squad?
I'd personally like a Batman game where the Joker is nearly absent after his death, where the only mentions of him are Harley on a rampage. Keeping in trend, Bats would only appear as a character you're bent on defeating (likely getting the ultimate upper-hand at the end), and only popping up at each villain's near-success with whatever dastardly deed they're up to. He'd almost act as the game's target rather than the anti-hero we've come to know, (play) and love.
The seedy underground of Gotham is begging to be explored. It would be somewhat of an Origins game, but not in the sense of the origins of the criminals. What you'd be introduced to was how the underground continues to operate even after Batman rounds up all of those baddies in every story. Maybe we'd even be introduced to how one of those daring prison riots goes down, as all of our villains make it back on to the streets and right in to their old habits.
The game could lead off with our villains; locked up, and right at the start of a jailbreak. A minor chain of events, say someone nabbing keys off Sharp's or Cash's belt loop, suddenly balloons and quickly explodes in to an all out war. The villains we've worked so hard to capture in every other Batman saga are now suddenly the focus of the story. The plot twist is, whomever this new, mysterious Batman is has become the player's worst enemy and greatest fear.
For once, the entire cast of characters trying to take over Gotham would have to put their differences aside and work together for one common goal. You'll spend the entire time discovering what makes each of these villains tick, all while trying to discover what has become of Batman after Arkham.