Either it was Reeve's creative decision in which case I've lost some faith in his cinematic vision for Batman, or it was a WB edict from jumpy execs who probably ask every new Batman director "Why isn't Joker the villain?" Either way, it derails some of my hype for the sequel.
I think Reeves indicated that he felt he nailed the casting and wanted to get something into the first movie.
Remember, Reeves supposedly already mapped out the trilogy, the Joker had to be in there somewhere and you're going to get burned no matter when you debut him. It's a pretty ideal choice to help illustrate that the other villains already exist and Batman has already met them with just a few seconds of establishing since everyone is already familiar with the Joker.
Doesn't mean that Reeves' Joker has to become the center of attention for an entire film though. The only compelling part of any of Leto's Joker, including when he was in the Academy Award winning Zack Snyder's Justice League, was him around the edges of Suicide Squad threatening to become the biggest problem of all. The comics very much love the idea of adding to Batman's problems by having the Joker free and loose while he's trying to deal with some other Gotham level threat because it's plausible for the Joker, and few other characters, to do pretty much anything the story demands. No Man's Land concludes all the arcs by having the Joker return to town as Batman and the GCPD triumph at restoring order. The Joker works as a "side villain" like few others because his level of threat remains so high with little establishment needed. You can have him interrupt a fight between Batman and the main villain by blowing up a building just because he thinks it's funny since people will accept that he did it because he's the Joker.
I wonder if Reeves could make an Arkham Asylum (game) movie work.
Like make it a horror film that takes place almost entire in Arkham where multiple villains have broken out. Not sure how you'd make it exciting with grounded non-power villains though.
The comics have done this quite often. Perhaps most famously in Grant Morrison's A Serious House on Serious Earth which I've just assumed someone is going to adapt at some point.