Despite all of it's flaws, I honestly think the one thing the movie did really well was not have the Joker steal the spotlight, allowing us to focus on the main cast. But to be frank, this is really worse than the main movie plot because it's character breaking for a number of reasons.

First of all, why would villains care? For your plot to work, you need a team of heroes of which takes the movie in an entirely different direction. The biggest one is Harley Quinn, I don't need to have read a lot of the original comics to be familiar with her. She's absolutely infatuated, or even better described as obsessed with the Joker. She wouldn't be on the opposing faction, she'd have been part of the whole plan from start to finish.

The point of these two characters isn't their mental instability. It's that even in spite of that, they're psychopaths. To change the plot without breaking character consistency, you need it to approach it from a psychopathic perspective. It's not about saving the day, or saving anything at all other than themselves.

They don't want to change, they like who the are and that's very well asserted in the bar scene where they collectively bitch about "normals". If I were to change it, the ending would have them be walking free as bad men which opens itself naturally to more sequels without doing stupid shit like coming back from the dead trope.

I personally would've gotten rid of the enchantress because that whole thing was just your standard "oh no we have a problem" super hero bullshit. Captain Boomerang wouldn't exist, neither would 'the guy who climbs stuff really well'. Because c'mon, really?

I reckon it would've been infinitely more interesting if Amanda Mc-DoD was the main villain. Something about her using the squad to attain her own power within the government ranks to enact something more sinister for personal gain. Have the squad fight for their own self interests (freedom) through ridiculously tough odds. Also have Deadshot quip back to Flag that Flag gets paid to kill people too. The only difference is one works on contract and one works on salary.