Can't do this without end-to-end spoilers, sorry...
There are a lot of ways to do a villain movie. You can hire a top-notch actor and make the villain so intensely hypnotic that the audience can't look away - think Silence of the Lambs. You can hire a very good actor and give the villain a deeply traumatic background and an unshakable conviction that he's doing right by his own measure - think Magneto as Holocaust survivor/mutant defender. You get the idea - give the audience something to hook into, and a sense that the villain is more than a string of meaningless malevolence, however dirty their hands may be.
One thing you do NOT do is try to make villains look good because the so-called good guys are actually really awful shits. Because that's just a lose-lose game. I don't like Oliver North better because his bosses were worse, nor do I like any of the Watergate conspirators better because they worked for Tricky Dick. In this movie, the bad guys end up working for Amanda Waller whom Viola Davis does a great job of animating and the script makes into an utterly despicable idiotic killer herself. Props for putting a tough female of color into this role, but zero points for having her senselessly murder her own underlings. I'm sorry, no matter how much she pronounces herself "consequences" or "the devil" or whatever, she loses credibility when the script has her acting in stupid and pointless ways. There's a moment early on where she says that her job involves getting people to act against their own self-interest for the good of the country and I'm OK with that. But beyond being hard-assed and tough and randomly violent what skills does this person have at doing that? How did she get to where she is? That she is exactly one pixel deep is emblematic of what's wrong with this movie (and a great waste of Ms Davis's talents).
It takes special skill to manage an ensemble cast and this movie lacks that. Only two of the characters are really fleshed out - Will Smith's Deadshot and Margot Robbie's Harley Quinn - and the Joker is iconic enough by now not to need an intro. Everyone else gets disconnected background scenes or ridiculous third-party talked-out intros (poor Katana, blah blah). El Diablo doesn't explain his background because of what he did and how he's dealing with it, OK. So someone needs to cover that. But you can only pull that trick once and have it work. Mostly I just wanted people to shut up and get on with the... well, I can't exactly call it a plot.
So, you have villains we don't care about fighting goop things that are all CGI and not terribly important. There's no sense of moral imperative either way. The weight of a decision to use killers and psychopaths as weapons against humanoid blobs is a lot less than if they'd actually had to kill real people. I understand that the movie was desperate to avoid an R rating (why?) but this choice really undercut any seriousness it might have had left. By comparison, the moment where Deadshot takes aim at Harley matters, not just because she's a star in this movie but because she's an actual person and the choice to kill her or not has real consequence.
Likewise, I hate how the ending wimped out on killing Enchantress/June Moon. Cara Delevingne does a decent job as a person possessed and hating what she has become but the important question is will she lay down her life (or be killed by the person she loves) in order to achieve something necessary? Compare her non-death scene with the real heroism of El Diablo, which I felt had meaning for a character looking for redemption.
Lost in all the clutter is the idea that this movie is actually a (very twisted) love story and explores some of what people will do because of their feelings of love. Joker and Harley play this theme to its insane hilt, but there's also the clarity of Deadshot's love of his daughter and how it creates strict bounds on his actions. El Diablo is driven to inaction and then action because he killed people he loved, and Rick Flagg's love of June Moone is his main motivation. I could even expand this circle by including Amanda Waller's love of her country and, sure, throw in Katana who is bent on avenging villainy using the sword that holds the soul of her beloved husband. If the movie had stripped away everything else and just given us these eight and let each of their stories develop we might've had something. Instead, we got a giant mess that takes longer than it should to go nowhere. I didn't hate it, but I did dislike it.
Footnote: This movie is likely forever to be my counter-example to my rule of thumb that having a single writer/director leads to better outcomes.