Nah, I don't agree. The basic story was fine. The problem wasn't what it was about, but what managed to get into the final cut of what David Ayer had planned. It's the execution that simply is missing, because too many pieces of the puzzles have been removed.
What? The very problem here
IS what the story is about, because it didn't work. You're right, execution is key: when you have a good idea.
The story is problematic automatically because it's too big. The Squad are the fall guys but if the damn world ends everybody's dead so that doesn't matter.
In the wake of BvS, of which SS acknowledges it clearly comes after, there's no way in Hell that Wonder Woman, Flash, Aquaman and any other heroes would sit by while the apocalypse plays out and a group of villains do their job, be it by government advisory or otherwise.
Come on, man, this story was doomed the moment this was made into a "save the world" endeavor. The Squad should not be engaging in stories that large. Because then you have plot-holes like this: why are supervillains doing the job of superheroes?
I'll say it again: the Suicide Squad should
NOT be saving the world. Their missions need to be far more street level, contained and nuanced.
That's how you tell a compelling story about supervillains, or at least as it pertains to the Squad.
So yes, the problem was very much always what this was about. From the moment it was stated in the trailer, I brushed off the "Let's go save the world" line thinking maybe it was just tongue in cheek but it wasn't. They really went there. And they shouldn't have.
The moment Ayer sat down to write and thought "I'm gonna put Joker in this, hire an actor to go all method and then make Enchantress the main villain" he ****** up.