I would take it back to it's roots and completely reboot it. It would be an amalgamation of the tones and themes found from the Burton films, Nolan films and the Timm/Dini animated series. The setting would be the late 1930s and while "comic accuracy/history" wouldn't be crucial I'd use it as a grid for the structure of my film. I would definitely have it begin with an opening WB logo with an exciting black and white period piece of a live action Zorro. You know, an exciting, adventure filled opening which would eventually take the audience from the Zorro film, to the audience that features Bruce Wayne and his parents. I'd try to make it as cheerful and optimistic as possible, like a typical family outing to the movies. Something audiences could identify with. Obviously after that, the events that would unfold would be tragic with a depressing tone. Have young Bruce start out as a cheerful, wide eyed, grinning kid, to a a child that witnesses the brutal killing of his parents (shockingly graphic to push the PG-13 rating), sadness but also anger. I'd play on the loss aspect of losing a loved one at an early age by showing things like the funeral, elders telling an innocent kid about the responsibilities that he'll have to have that a child shouldn't have to worry about and ultimately, the bed side vow/prayer that Wayne makes that Alfred would catch secretly and worry about. I wouldn't spend too much time, but I'd definitely start out with an emphasis on Wayne's loss. I'd try and keep the mental and physical training to a montage that would express just how far one would have to go to devote themselves to become Batman. The main story would take place early in Batman's career. He would face mobsters and weird, crime doctors. He would have the "feared, creature of the night" persona just as the original golden age Batman. Police and public support would be minimal and played up later in other films. The main villain would be Hugo Strange using "Prey" as reference. I would utilize elements of the sinister, crazed doctor/scientists from the early comics as well as the modern approach for Strange. This is a man obsessed with Batman. The film would really delve deep into the psyche of Bruce Wayne and Batman, what better character to provide that exploration than Strange. Also beneficial is the fact it wouldn't be a villain we've seen before. Joker would only be hinted at with a "pre-Joker" encounter with a mob fight at a factory, perhaps one of many hired muscle to take care of a problem for Strange who has connections with the mob (Rupert Thorne, Maroni, take your pick).
By the end you'd get a complete understanding of what goes on behind the cowl of Batman. The obsessions, the guilt, the power, etc. By the end, you'd just want to comfort and hug this kid that lost what was must important and crucial to him while at the same time, being impressed, frightened and in awe with the Batman persona he created because of it. It would be very "parent centric" and wouldn't end with Batman on top of a roof top again.
A future film would most likely include the Joker. In fact, if you set up that Batman created him in the first film, subtlety to the audience, you could play on that with the film. Suppose it is a factoryesque scene (Ace Chemicals/Axis, whatever) in the first and it's just a nameless thug you see get thrown in. The second film can go in deeper to who exactly that was that the audience saw.
The sequels would be about Batman, pathos and how the villains directly mirror and represent Batman's personality, WHILE being period pieces. Want to see what Batman would be like in the 50's, 60's etc. like in the comics? These films would express that. Batman would change with the times so to speak the first being the 30s. You could easily have a Batman in a costume in the beginning, one that can take 30s pistols and weapons without armor (either by getting hit or simply dodging) to one that would require armor. The key thing would be evolution.
