This movie is plagued by puzzling structural decisions in its storytelling, and the bar scene is perhaps the most glaring example of how the rushed pacing and redundant exposition of the first act (did Deadshot really need to be introduced three different times?) winds up crippling critical moments later on.
The bar scene, which should have been a pivotal turning point and one of the movie's most emotionally resonant scenes falls flat, because there wasn't enough time spent developing the relationships between these characters, and the “we’re in this together” camaraderie that emerges rings false because it was never really earned. When the premise of a movie involves throwing a bunch of criminals together against their will, with no reason to trust one another, showing how that trust builds is paramount in establishing motivation and achieving a certain level of plausibility. This never really comes together, unfortunately. The only thing that saves this scene is the chemistry between the cast. This could be said of many moments throughout the movie; their ease and familiarity with each other off-set translates to a solid, natural dynamic that makes up for the substance and coherence the writing and editing lacks.
It’s a shame, because in an ensemble piece like this, finding a cast with the right chemistry and presence is one of the most important elements to get right, and often one of the hardest to achieve. There’s so much potential here that could have been realized with a different script, under a different director and studio.
As for the Joker being underused with tenuous connection to the plot, this could have been remedied by switching his function within the film from simply being a minor supporting role for Harley, to being a larger thorn in the squad's side. He didn't necessarily need to be the main antagonist (though I do think a more down-to-earth villain, as opposed to an otherworldly extinction event, would have better suited the story), just a bigger obstacle in their way.
Consider how it could have augmented the story: The skeletal relationship between Rick Flag and June Moone attempted to provide an additional layer of drama within the main conflict, where Flag finds himself emotionally torn between completing the mission and potentially destroying the person he loves, or throwing the fate of the world to the wind, but due to disjointed pacing preventing any real character development from happening, it misses the mark. This same sort of dynamic could have arguably been achieved to greater effect with Harley and Joker, whose relationship is more solidly established. (cf. Assault on Arkham)