So, I was bored and baked, so I figured, why not? Someone should make this. It's the Zen of Batman games.
The controls would use pretty standard free roaming controls. Just running around the city, the face buttons would be keyed to regular combat - a low hit, a high hit, a jump (which could be used for a double jump or, I don't know, a glide?), and a context sensitive button which would be used for interacting with objects, stealth takedown, or a grab/disarm when facing a bad guy. The left analog stick is movement, the right analog stick is camera. There'd be an auto-lock for Batman's gadgets, with the triggers being used to scroll through targets, and a gadget assigned to either shoulder button. So, for say, batarangs, just hitting the shoulder assigned to it would fling one at whoever you're targeting. Smoke grenades or grappling hook or whatever would probably have to use a double tap. And you could maybe shift through the assigned tools with, Idunno, the arrow keys.
Tapping in the left analog stick would toss the camera right over your shoulder and let you free aim. Tapping the right analog stick would shift you into a close combat mode, the idea being that you sacrifice the camera control in place of having attacks keyed to the right stick. You remember that scene in Batman Begins where he's completely circled by a bunch of thugs and he's just this whirling dervish of bludgeoning limbs? The system would be there to help you juggle that kind of multiple combat without just getting collectively beat down any time you're swarmed. Basically, you just click the right stick in the direction of the guy you're attacking. A quick tap would work as a rabbit punch or a quick disarm/deflect, a heavier punch with a harder contact tap, a sweep around the outside of the stick to pull off a sweeping move, etc. The trick would be to juggle the thugs attacking you by throwing quick hits to knock back swings your way and try to fit the heavier, disabling blows in between. As for movement, it would still be keyed to the left analog stick, but your movement would be centered around whatever enemy was targeted, with an invisible circle around the perimeter of the target, so left and right would strafe in the circle around the target, while forward and back would approach and retreat, and snapping both sticks forward would initiate a tackle. So you could also use the system to zero in on specific enemies and target them more precisely for close quarters combat. I think all in all it would make for a basic control system that would lend itself well to free-roam *** kicking, mild stealth, and arcade style boss fights.
Onto mission structure. Ideally, you'd approach the game's production in a similar way as Dini and Timm did with Batman: TAS. You establish a separate continuity behind the vision of a creative team that allows you to reinvision Batman's rogues in ways that will make for more interesting gameplay possibilities, and also leave the door open to expand the universe with other DC Universe games (like the Superman series spun out of the Batman series). Place it in year two, letting you introduce the villains for the first time and present a Batman who's not bogged down by too much continuity. Each rogue has his own series of missions that each tells an independent story. Sometimes missions are automatically unlocked after completing an earlier mission in sequence, while others require you to follow leads, which are freeform challengers on the map - investigate a series of warehouses, shaking down thugs from a certain neighborhood, shaking down dealers, etc. Maybe you have a bank of leads to follow for each of these intermission portions - some of them might unlock the next mission, some might yield other rewards. You could split the year up into four seasons, with say, the finale of two storylines playing out in each season, but missions from the different stories stretched throughout the timeline. Side-by-side, you can have Mafia gang war missions, Bruce Wayne missions, Commissioner Gordon missions, etc. And then you have to tie together all these things to make a cohesive story….. But it could totally be done, and it would be epic. You cap off each storyline with some sort of wicked-explosive boss battle.
Finally, the city just needs to be alive. Batman beating up crooks in an open Gotham city would be just plain awesome, but it's even more awesome if your crime fighting has an effect on Gotham. So you break the city down into neighborhoods, and you give each one a crime index. The more you enforce your brand of awesome justice in a neighborhood, the lower the crime - leaving a slum to fester will cause crime to boom and start spilling into other neighborhoods. Graft on a basic Monopoly-style system as well, based around Bruce Wayne's wealth. You've got property all around town, and you can buy/build more or unlock it from missions. You have different structures you can get, so a police station might cut crime in the area, an office complex might increase your income, and a research facility might unlock more gadgets or vehicles. Most of your money comes from a revolving income based on what you own, but you keep the whole aspect streamlined and simplified. Money can be sunk back into buying more property, equipping yourself, buying upgrades, that kinda stuff.
I also think if you had the system in place, it would really lend itself well to producing cheap, episodic content using a tiny dev crew. You could, for instance, very easily put out a quarterly Year One story between production cycles, or even tinker the system to do some cool sort of GCPD or Gotham Underground thing.
At least, I don't think it did. 
