If this were my baby, if I was "in chahge", I'd reboot the whole damn thing and go back to square one. No Blake, no Bale Batman, no Catwoman, no Nolan, no Burton, nothing. All new.
I would take it back to it's roots. I think a period piece would be a great way to go about it. A late 1930s Batman (not the characterization that kills and has a gun of course, just the time period). 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. Why not modern? Batman could never exist in a modern setting, not with today's technology. He'd be shot and killed, spied on, figured out. His identity would never remain a secret. Taking it back to the character's introduction would make it more believable.
I would have it begin with an opening WB logo with an exciting black and white period piece of a live action Zorro (silent era title/story cards and all). Audiences would be like "what the ****, I thought this was a Batman movie". It'd be an exciting, adventure filled opening which would eventually take the audience from the Zorro film, to the story 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 at the movies. Some good clean swashbuckling, cheesty fun, 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, enjoying his hero on the big screen, to a a child that witnesses the brutal killing of his parents in a cold wet alley in Gotham. Not just sadness but anger too. I'd play on the loss aspect of losing a loved one (or in this case, both parents) 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. Holidays like Christmas and birthdays without anyone to share it with. I think the bed side vow/prayer that Wayne makes would be an important aspect too. Burton and Nolan never show this, but, what if Batman started as early as the death of Thomas and Martha Wayne? A vengeful kid that's oblivious to the real world, making a vow to rid the world of crime. Maybe have Alfred catch this secretly and worry about this kid's mental health. I wouldn't spend too much time on it (origins have been done to death), 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 (Gordon, no Gordon?).
As far as villains go, I think Hugo Strange would be a good one if you use "Prey" as reference. 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. With Strange you can explore the psyche of Bruce Wayne/Batman and get really intimate with what may or may not go on in Batman's mind. Does he do this because of his parents? Does he do this because he's crazy? Is this "heroic" persona just some immature quest because he was a child that just got out of a movie (the Zorro film and the death of his parents fuse together). What is it that makes him tick?
For characterization, I'd make Batman a cynical *******. A sort of byronic hero. He'd be that that guy in the corner nobody really likes, the guy that's always right and two steps ahead. He's dedicated and trained to do this, so why not? The point here is you'd question his sanity. It would get to a point where Alfred questions his surrogate son's sanity because of the determination he has against fighting crime. One extreme, and this is just a thought, is that he rarely leaves his suit. He has a stench/odor that emits from it suit and has this refusal to leave his surveillance/computer while in Bat garb when not on nightly patrol. Basically bat-____ crazy.
He'd wear the suit like it was his second skin and obsess over the quality of his equipment for his war on crime (perfectionist/obsession). Think of a kid that takes dress up or halloween too seriously. Only time he'd be out of it would be during the day or in any situation that calls for him to be Bruce Wayne. It'd be so sick that he'd make a rule that when he's in the Batcave Alfred must call him Batman and Batman only.
He'd be cynical, cunning and self loathing. Basically an immature child that never grew up with an obsession with vengeance, justice seeking, and adventure. He's just on the verge of being a crazed lunatic like his enemies and may suffer from multiple personality issues. The thing that would pull him back are his parents, their ideals, Alfred and the well being of allies.
His charisma would come from his drive and dedication to rid Gotham of crime. Something that could never happen and would be his plight or curse. He'd have to have pathos or else audiences would never feel for a man that sits sulking in a suit all day waiting to eradicate all forms of crime (especially if you play up the extreme qualities of him). To identify with him you'd have to inject a theme of loss of childhood and nostalgia since Bruce Wayne had it taken from him. The last thing he'd experience before the devastating loss of his parents would be film, specifically the swash buckling, adventuring do-gooder, Zorro. Which, along with a fateful evening with a large bat bursting into his study, would be the source of his alternate persona, Batman.
For Strange I would utilize elements of the sinister, crazed doctor/scientists from the early comics as well as the modern approach for Strange. I'd definitely have a moment in there with him dressed as Batman. That would be his motivation, to become Batman. He'd be just as sick as the nut jobs he analyzes and diagnoses.
Every iteration of the story/character has the Joker, he is Batman's history. For the Joker I'd hint at him 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). No make up, no bleached hair/skin. Just a regular guy. Maybe not Red Hood, maybe not "Jack Napier" but someone associated with the mob. Maybe in the first film when Batman goes in, trying to stamp out Strange/the factory, this guy gets punched/thrown/dropped over a catwalk? Falls in chemicals? Not sure. Maybe have a moment where Batman is the cause but since he's fighting so many opponents so quick (like in Batman Begins) he doesn't notice the damage he's doing. The fall wouldn't be important (in this film) and wouldn't linger, but it would be enough for audiences to go "hmm, is that supposed to be the Joker?"
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, his family, his upbringing. At the same time though, we'd be impressed, frightened and in awe with the Batman persona that he created from that trauma. That will and dedication. It would be very "parent centric" and wouldn't end with Batman on top of a roof top again. Their graves?
To reach this point though, Strange would be the catalyst. Imagine a scene almost as iconic as the interrogation scene in The Dark Knight where the two characters are meeting. Perhaps Batman "in the chair" with Strange discussing his past, but not willingly.
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 (as I said above), 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. Have a second film intro (think the LOTR Two Towers intro where it takes the audience back to the first film with a new POV) back at that factory with Batman from the first, but instead of following what Batman did (going after the thugs), we focus on the guy he knocked over and his journey through the toxic waste and coming out the other side as the Joker? The Killing Joke perhaps?
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. Changing with the times and technology.
Grayson, The Dark Knight Returns in a third or fourth or fifth film that takes place in the 80s? All possibilities. That's how I'd start and continue a series for the franchise.