Beware of unmarked spoilers
Harley Quinn’s interactions with the Joker will be set after the events of the series.
She takes him to the portal after all is said and done and most of the show is her telling him the story.Batman will make a cameo chasing Joker and Harley.
There will be a sequel series of another DC character getting Isekai’ed.
Most likely the Justice League.Clayface will betray the Squad
How do you keep a suicide bomb in or on someone who can turn into and regenerate from sludge? You don't, which makes Clayface the most likely candidate to be a turncoat when he realizes he can live the high life in isekailand by betraying his "comrades".At some point, Clayface will be disguised as one of the leaders of whatever enemy faction the Squad has to face down
Another obvious twist, considering the FukuJun casting.Fione is Harley’s Alternate Self from the fantasy world.
Which is why she spent some time gazing at Harley in subdued surprise and once the Squad finds out, Waller is going to order them to take full advantage of that fact by setting up a Bait-and-Switch-trap for the Big Bad which includes putting Fione in Harley's outfit and vice-versa. the reveal of the switch being made when "Fione" sports Harley's crazed smile before getting the jump on the target. The main villain of the fantasy world will try and enter the Suicide Squad's world at the end.
Perhaps to escape the punishment they would have gotten in their original world, they believe the gate would allow them freedom and a brand new world to conquer, as they pass through. Eventually, they would end up defeated again for good and end up as an inmate in Belle Reve to serve their time there for the crimes as the gate have been closed off at that point.