I have seen a LOT of criticism for this game, some valid, and some... just plain stupid. So here is why the game is actually a mess. (SPOILERS BELOW)
1. Characters being WILDLY out-of-character.
In the game, there is recordings you can find throughout the open world that explain how the JL came to be corrupted by Brainiac. This is all well and good if...it didn't make them seem so stupid. Diana and Bruce BOTH recognise it's a trap when Brainiac invites the League for open negotiations on his ship, and Superman says they should go anyway, 'in good faith'. And even worse, rather than only sending 1-3 members as espioenage, all 5 of them go! Completely unsurprisingly, Brainiac traps the League and starts his corruption process, but Flash and Diana are the only 2 to escape. Which is where the second problem arises.
2. Batman and Wonder Woman's roles in the Story
Flash and Diana both escape, but have to leave the other 3 league members behind. The problem with this, is that it would have better served the story if it was Batman who escaped instead. Think about it, we as the players and the audience have spent more time with the character, know more of his history and his capabilities as a result, and it also would be a better usage than how he was portrayed in the story. This would've also been a better explanation for how the Suicide Squad get the 'anti-JL' gear they pick up throughout the story.
3. Brainiac
Brainiac's treatment in the game, is... in a word, odd. They say he's this all-powerful genius who easily overtook the League, but when you actually end up fighting him, all it is is really a redo of the Flash's boss fight while occasionally blowing up machines and goons. Which is a huge disservice to his character and fails to show what he is really capable of.
4. Killing The Justice League
Obviously, as the title of the game says, you kill the Justice League. And while I understand that's the entire point of this game, the problem is that this is supposed to be our FIRST exposure to the Justice League of the ARKHAM Universe. If it had been totally disconnected from the Arkham Universe, there wouldn't be so many problems with the story. I have seen many theories that the JL we kill could be clones or even possibly end up replacing them with alternate earth versions of the dead JL members, and honestly if this was the case, I'd be fine with that. But the fact that this is the Arkham Universe is a MASSIVE problem for the game, despite it likely being a decision made due to Corporate Interference.
5. The Multiverse
After killing Brainiac in a pretty anti-climatic fashion, the Squad is told that there are 13- oh I'm sorry, 12 other Brainiacs on alternate earths. No doubt the players are supposed to kill the 12 other ones across the various updates, events, and seasons of SS: KTJL, since it's a live service game (which was another decision that really shouldn't have been made) but what about after that? What content could they add to fix or renew interest in the game? I don't know. And I don't think even the CREATORS know, either. The game feels totally unbalanced, has a problem with telling instead of showing- something a lot of media does- and disrespects almost every single character in the game that we have any form of interaction with.
HONOURABLE MENTIONS:
The UI of the game is crowded and clunky, with numbers and visual effects flying across the screen and breaking immersion. And this isn't an exaggeration either, take a look:
Which makes me as an autistic person with a pretty bad sensitivity to light extremely overstimulated. It's also terribly overdesigned.
Conclusion:
Suicide Squad: Kill The Justice League is a terribly written, overdesigned, shoddy mess, which does a huge disservice to the characters used in it, confuses the players with its nonsense story decisions and makes the main antagonist and deuteragonists of said story seem incredibly stupid. These are the main problems with it. Not the Deadshot 'retcon' (you know who you are)