I think the biggest difference between what X-Men does (from what I've seen) and what happens in Mankind Divided is that the X-Men are constantly being portrayed as being victims of an unjust system. I never really felt that way playing as Adam; there's no solidarity shown between Adam and his fellow augmented in the way there was within the Mutant community, only sympathy extended out of a general sense of kindness, and that's only if you decide you actually want to go out of your way to help them.
The lack of general character development also hurts this; Macready never really changes his opinion on augs from what we see, Miller never really cares about you being augmented in the first place so he never really comments on it, the one other augmented character on your team is a totally optional side character you can ignore, and Marchenko has no nuance to his motivations, no self-righteous justifications for his violent actions, no remorse or conflict over targeting members of his own people, etc. It feels like all the cruelties that are happening occur off-screen while everyone in the main story ignores it. I will say that some of the side quests do a better job in fleshing this aspect of the game out.
Character development points are legit, there just wasn't a lot of time or heart put into the plot and characters honestly, but the reason that Adam never feels like a victim of an unjust system is because he isn't.
He works for interpol, being vouched for by people in the world like Sarif who, while himself being augmented, still has a lot of cultural cachet and power. His body doesn't reject his augments so he has no need for neuropozine, which is another avenue for the system to exploit and subjugate the augmented.
The only roadblocks in Adam's way, are literally that; the way the ordinary police will stop and ask him for papers when he uses the "wrong" entrance. And it's just a bureaucratic nuisance because he always has the right papers.
It's the fact that Adam has roots in both the subjugating system and the subjugated that marks his unique position as the protag, otherwise there would be no meaningful choice to make in the game. If he was just an ordinary augmented, he'd take their side every time.