Infamous: Second Son had plot issues surrounding how the conduits were handled, and I feel like it's so close to making something much more interesting of the situation. First off, conduits continuing to exist at all is a retcon from Infamous 2's heroic ending, but that I don't care as much about because that's a result of the devs underestimating the number of people who would go for that ending where you basically have Cole kill millions of conduits (including himself) to save billions of humans as opposed to the evil ending where he does the reverse and becomes The Beast. If we need a little retcon to have the game exist at all, go for it. Past that very first step, however, is where issues begin to show.
The basic outline of the plot is that conduits (empowered humans) are still around, and they're feared and discriminated against by the government. Their oppression is often primarily carried out by the Department of Unified Protection, or the DUP, which is a federal agency tasked with rounding up all conduits and detaining them as bio-terrorists. Ironically, it is led by an extremely powerful conduit with the power to control concrete, Brooke Augustine. The main character is a Native American man named Delsin Rowe who initially appears to be a smoke conduit, but in actuality his ability is to absorb those of other conduits. He's discovered, so the DUP swoops in, Augustine tortures him for information, doesn't get the answers she wants, and then tortures/cripples the rest of his tribe by growing concrete out of their bones which will eventually kill them basically out of pure sadism. Augustine's hidden agenda causes this to make basically no sense, but we'll get to that later. This kicks off the plot where Delsin travels out to Seattle, with the plan of accumulating enough power to take on the DUP directly, steal Augustine's powers, and use them to fix his tribe.
Now, as for Augustine's hidden agenda. It's revealed right at the very end of the game pretty out of nowhere that her real angle with all of this was to protect conduits from the military. In her mind, it's best to imprison all the conduits so the army doesn't go after them, while she can safeguard them in her own way and stop a total genocide. DLC later elaborates that in addition to this, she engineered certain conduit breakouts because at one point the DUP had just plain old captured all the conduits, causing the government to decide they didn't have a purpose anymore and moving to shut them down and transfer all their captives into military custody. To avert this, she secretly allowed for certain dangerous conduits to escape and cause chaos, so that her agency could save the day and prove they should still exist. You may notice that this doesn't explain why she just randomly tortures Delsin's entire tribe for no reason when he was fully willing to give himself up for their safety, a decision that leads to her downfall. I guess she's just racist. It also doesn't explain why she sponsors a bunch of inhumane experimentation on the conduits in her custody. She's the head honcho here and she supposedly is truly interested in their safety. She could just not do that. Revealing this motivation so late into the game without any real buildup is itself a very strange decision that makes me wonder if it was also just a super late addition in the writers room given how it contradicts what otherwise just seems to be a power mad sadist, but I think it's a failed attempt to recreate the last minute reveal with their main villain from Infamous 1 (which is that he's a future version of Cole MacGrath, the protagonist, who did what he did to jumpstart Cole's power development to prepare him for what's to come in the future including killing Cole's/his girlfriend) which I feel worked much better. Regardless, this isn't even where the issues with that sudden motive end. It's not just contradiction, but that they don't even make a whole lot of sense on their face given her capabilities.
Second Son I feel suffered from an attempt to have their cake and eat it too when it came to conduit power levels. They wanted their conduits to be super powerful for gameplay reasons, and I can get that. It's fun to have these impactful abilities that put you so far beyond humanity, and it allows you to design more interesting and varied enemies than just different types of real world military forces. However, for story purposes they also want conduits to be weak enough that they can be meaningfully oppressed by humanity at large and that despite their supernatural abilities, they're the underdogs. This is irreconcilable with things like a neon light using conduit being able to move at the speed of light and convert people directly from matter to energy (which is an insane amount of energy, there's a reason antimatter whatever is so popular in sci fi) and Augustine's a particularly bad example of it. She's ambushed with a rocket launcher by Delsin's brother (iirc) at one point and just sorta facetanks it, she can conjure giant concrete offshore platforms with a thought, and I'm pretty sure there's a statement somewhere that she's the strongest conduit seen since Cole MacGrath (the protagonist of Infamous 1 and 2) who at his peak literally hit harder than a nuke. Augustine's little scene showing her initial corruption has her and a little girl paper conduit wandering around a desolate city, trying to find a place to go and escape the chaos when suddenly the army bears down on her. She makes the decision to betray the girl, imprisoning her in concrete for the army to take, as the first step towards essentially becoming controlled conduit opposition. This is pretty dumb when the game otherwise establishes that she's so powerful that if she was to take on the army she'd just win. Small arms aren't a threat to her even without super mega concrete powers or trying to extrapolate from the matter-energy conversion girl, and she didn't even subtly free little conduit girl until like a decade afterwards, so if she really was just fearful of what would have happened to conduits what the fuck is she doing. Furthermore, pretty much everything that makes the DUP a threat is due to her. The ability to imprison conduits in the first place? She can just create these special prison complexes in the middle of open water and her concrete ostensibly disables the abilities of conduits. The ability for normal soldiers to not just fold to superpowers? She can bestow a weaker version of her powers to her men, basically turning the entire DUP force into mini-conduits. She's scared of oppression that only she could even possibly carry out, and the game doesn't recognize that. It also makes the heroic ending where she's arrested (for what? nobody knew about the engineered break out lol) really weird because the only reason those prisons can hold conduits is herself. She could literally just leave. And yet, despite this sounding like a mess, I feel like it's so close to being something much more interesting.
My proposal doesn't actually have to change that much. You can keep most of the power creep if you want (maybe not miss speed of light) with this. You can also keep the apparent sadism with this, and make it much less out of nowhere. You should just drop hints of this hidden agenda throughout the game. Brooke Augustine was a soldier herself before she got her powers, and you can have her be pretty deeply affected by this. A lot of military training is psychological, drilling the heavily regimented lifestyle and unwavering respect for authority into a grunt's head. It works as an exaggerated microcosm for society as a whole, where comfortable complacency is broadly preferred towards high risk and uncertainty. Therefore, make it so that the reason she doesn't fight the military off when they corner her and the kid is because she doesn't want to cross the Rubicon that forces her to enter a new world she can never return from. She doesn't want to fight the powers that be which she's so used to living and serving under. She, like most people, would much rather things just go back to normal. She'd rather enjoy mediocre security than take a big risk to fight for a fairer but more uncertain future, and this fear of taking a leap into the unknown and truly taking responsibility for her own fate is what keeps her in check, not really the fear of a conduit genocide which she's powerful enough to pretty much singlehandedly stop. Over time, she acclimates to this role, accepting the atrocities and abuses that go on under her reign, because there's always someone above her she can defer to. It's just the cost of doing business, and it's far better than the unknown. You can even keep the rather absurd situation where she's pretty much the sole lynchpin holding practical conduit oppression together as the end stage of this mindset she's developed over years and years of doing this, because some people just really do end up like that. Deep down, she just doesn't accept she's as powerful as she is both physically and institutionally because that's just far too much responsibility for someone like her to have. She really could just tear the system down by saying no, but she never will because of psychological conditioning that's gone on her entire life, from her time as DUP head to her time as a soldier to even her time as a normal American enjoying the creature comforts of modern life. This learned helplessness would put her in direct contrast with the protagonist, a rebel willing to throw caution to the wind and throw himself right into the fray in hopes of tearing it all down because he's got nothing left to lose, it would give the game a much more interesting message about freedom, fear, and the psychology of the intersection between the two concepts, and it really wouldn't even need to change that much about the setting. The fact the game is so close to what I consider a far more interesting idea is why I'm posting this here. The writing potential was certainly there, but instead we just end up with a really weird and contradictory character.
Got some other issues with the game, often gameplay related but another thing I don't like in comparison to Infamous 1 and 2 are how your karma level doesn't feel all that impactful on your day to day life, but I think this is enough text in one post on an old PlayStation game for today.