Ben Affleck's turn as Bruce Wayne/Batman is one of the widely-praised elements of Batman V Superman: Dawn of Justice, thus ushering in a new era for the character on the big screen in the process. Affleck's Caped Crusader next appears in a handful of scenes in the fast-approaching Suicide Squad, before he returns to the spotlight in Batman V Superman director Zack Snyder's Justice League in 2017. Sometime after that, "Batfleck" will be headlining his own solo movie set in the DC Extended Universe, too.
It's been known for a while now that Affleck is co-writing the DCEU's Batman solo movie with the newly-appointed DC Entertainment President Geoff Johns. However, during the Warner Bros. Pictures presentation at San Diego Comic-Con 2016, Affleck was finally officially confirmed as the film's director, as long reported. Hence, it will be fully up to the Oscar-winning actor/filmmaker to figure out on the direct connections between his Batman film and the other DCEU installments, Suicide Squad among them.
Jared Leto plays The Joker in Suicide Squad and told the Toronto Sun that he hopes that film is but the beginning of his run in the DCEU, saying:
“I hope it’s an introduction (of the Joker) … and not the end! Because I could easily just play the Joker a couple more times and then retire. Because it’s so fulfilling and so creative and it’s so imaginative. It’s really difficult to think about doing anything else!”
The Oscar-winning Leto went on to express his hope that his version of The Joker pops up in Affleck's Batman solo film, among other DCEU movies:
“I think it would be incredible to see Batman and the Joker go head-to-head! This Batman and this Joker. I mean, I don’t know, that might be too much! But that would be fun.”
Batman/Joker stories are well-trod territory for not only the Caped Crusader's live-action film appearances (see Batman (1989) and The Dark Knight), but also his animated movies (Batman: The Killing Joke being the most recent example). That's not to say that Leto's Joker won't appear and/or be referenced in the DCEU's Batman solo adventure (see the one-off nod to Batman's history with Joker in Batman V Superman). With Affleck acknowledging that the Batman movie property has already "been reinvented so many times", though, it seems unlikely that he and Johns would make Joker the central focus of the film's narrative, for related reasons.
Still, Affleck has also said that his Batman solo movie will further explore the Caped Crusader's prowess as a detective, implying that the film's storyline could see Batman undertake an investigation deep into the underworld of Gotham City. It wouldn't require a huge stretch of the imagination to envision Batman crossing paths with Leto's Joker (or seeking him out as a source of information) in the process of his investigation - so again, Joker could easily show up, even if he's not Bruce's primary antagonist in the film. If Affleck's movie takes place in Arkham Asylum as rumored, then Leto's Joker could even be a resident of Arkham.
As for the possibility of The Joker returning in a potential Suicide Squad sequel next instead, Leto has already discussed that possibility himself:
“If people like ['Suicide Squad'] enough. But, you know, the Joker’s not officially in the Suicide Squad, so they could make another Suicide Squad movie and have somebody else (as the wild card villain). And I would be sad not to be part of the fun.”
Suicide Squad is scheduled to arrive in theaters on August 5, 2016, followed by Wonder Woman on June 2, 2017; Justice League on November 17, 2017; Aquaman on July 27, 2018; an untitled DC Film on October 5, 2018; Shazam on April 5, 2019; Justice League 2 on June 14, 2019; an untitled DC film on November 1, 2019; Cyborg on April 3, 2020; and Green Lantern Corps on July 24, 2020. The Flash and Batman solo movie are currently without release dates.