Honestly, if it were up to me, I would go darker and more violent than any of the other Batman movies. Not necessarily gory or graphic but the villains would kill more often (on-screen, not implied), be more violent/heartless and nobody would be off limits. Particularly the Joker. I want it to remain serious, grounded and mostly realistic, though I would possibly do some of the less realistic characters as well. I would also want to see more iconic type visuals, moonlit skies/skylines, ghetto/streets, dilapidated buildings and more visually stunning action scenes.
If I were to create my own Batman universe I would start with a Batman solo film, where he is pitted against someone other than The Joker, then do a Joker solo film. Then two following Batman's sequels, where the Joker is prominent in each one. I don't like the idea of killing the Joker off or sending him to Arkham, ending his storyline, all in one movie. I would like to see them build up the rivalry over the course of at least 2 movies, bringing the rivalry to boiling points and intense show downs.
The Joker solo movie would start with the Joker being a serial killer before he becomes the costumed Joker. I would start with him being without the makeup as a serial killer/mass murderer. A mixture between serial killer and terrorist, attacking pretty much anyone on a whim and it's fun to him, he enjoys it and makes fun of his victims and crimes, but in a serious tone, not the over the top silly way he is often portrayed. An origin movie that starts there, but still doesn't go into why or how he became a serial killer or give him a name, it just starts in an opening scene of him stalking a victim at night, entering their home and killing everyone inside. Then at some point he is arrested by Batman and/or Jim Gordon, and sent to Arkham. They classify him as a John Doe, because he has no fingerprints or records available to them but they sentence him anyway. While in Arkham he becomes obsessed with revenge on Batman/Gordon. At that point he comes up with idea to become the Joker which plays on his already murder-spree-for-fun personality to counter Batman's suit. Maybe he's in Arkham playing cards with other criminals and sees a Joker card and comes up with the idea to use that as his image to get revenge against Batman or maybe it's a nickname that other criminals give him in Arkham as he gets into fights/kills other prisoners while laughing insanely/poking fun at their deaths. Then he meets up with the crazy but naive Dr. Harley Quinn, who helps him escape Arkham. Once out of Arkham he starts to dress as the Joker and starts to commit murders/crimes to attract Batman's attention, they have a first show-down as Batman/Joker but the Joker escapes and that would lead up to Batman 2, where Joker is the main villain but starts recruiting other Batman rouges in plots against Batman.
In the 2nd Batman movie I would have the Joker team up with 1 or 2 other villains. Penguin would be one, having him be a crime boss that owns the Iceberg Lounge, a Godfather/Tony Soprano like character, that's nicknamed the Penguin based on his look, not some kind of deformity where he is part Penguin.
The 3rd Batman film I would do an Arkham Asylum like movie, where The Joker leads a band of Arkham criminals (the criminals from the previous movies and a couple others) in taking over the prison and Batman has to defeat them to gain back control. Or they come up with a plan to escape Arkham and takeover Gotham. There are hundreds of ways to band them together and make them pose threat to Gotham/Batman.
You could still have up to 6 different main Batman villains in this Batman Trilogy/Joker film, with complete backstories and story arches and then one final showdown with the villains banding together against Batman. At some point I would introduce Nightwing to help Batman, maybe others, because 5 or 6 villains (plus their henchmen) against Batman alone would be a bit much.
Obviously just a baseline of an idea but it's something I would love to see. I know alot of people would say that's over-saturating The Joker (plus I'm sure the final group of villains together would get the typical "too crowded" complaints) and think it would become redundant/boring but I don't care, I want to see these two characters (Batman/Joker) form a distinctive and definitive rivalry and I don't think it can be done in 1 or even 2 movies, at least not the way I would like to see it. They have a long and storied rivalry in the comics and I would like to see something like this to introduce that rivalry to the big screen. It wouldn't be kid friendly at all, which would probably diminish box office numbers but I'm not a kid anymore, this is the type of Batman films I'm interested in seeing.