diving into actual spoiler territory for like most of the prominent series he's worked on (ze, aitsf, and some minor stuff for infinity i guess):
it feels really disheartening that proportionally most of the characters with disabilities that actually feel the impacts of them are also villains. don't think i've forgotten that lol! we do certainly have characters that are heroic like snake (who is basically unaffected by his blindness and prosthetics) and sigma (who is completely unaffected by his prosthetics in vlr) and bibi (who, to be fair, is affected by her chronic health issues). and to be clear, i wouldn't prefer them being written as if they were completely incapable, that's ableist in its own right and i think that of the two options the first is the better call. but most of the characters who do actually get to experience the fact that having disabilities can feel debilitating or impact your life are also evil.
hongou is probably not as big of a deal compared to the later instances, but it's still kind of a bad look to have the main villain that abused children motivated by a desire to use the morphogenetic field as a method of overcoming his disability. i know it was discussed that he also suffered trauma via gordain's nonary games too, but that is not presented anywhere in the story itself and is mostly just external information from a q&a. again, it's not as big of a deal as the rest of the stuff going forward because they do play a little bit with the "junpei, they call that prejudice." thing to mock the fact of him hiding behind his disability when he did murder three people, but it's still worth critiquing as part of a pattern of behavior.
saito sejima is probably the most ableist character he's written in a game i've personally finished. this doesn't mean i don't find him compelling and that there aren't interesting things about him in the context of his relationship with so and date. there's an implicit understanding that saito could have turned out better if he'd been medicated, if he'd been given a support system, and if he'd been raised by somebody that was not so sejima. i think this is probably the part of his character i like the most. however, on a level beyond the subtext, he was written as a character that was fundamentally destined to become evil due to a neurochemical disability and that this was only allowed to continue because there was nobody to intervene. he derives pleasure from murder and only murder, and the thing that would fix him is having that missing neurotransmitter supplemented regularly. the only reason he feels the impact of that disability is because it creates the narrative's central mystery, and the impact itself is (of course) his twisted personality.
i have not finished remember11, but the (admittedly brief) tweet that inspired me to write out my feelings on this was a reply to another tweet critiquing kodaka and uchikoshi's writing of disabled characters that said something along the lines of "remember11 is genuinely more ableist than everything kodaka has ever written combined". to be fair, i can't verify if this is true! however, the central premise involves a criminal psychology major who is fixated on a serial murder case committed by a child with DID that she believes might be faking to gain a sentence lightened by insanity, so my spirits are not lifted.
honestly, there's also always something that really complicates my feelings on this casual ableism in every game i've played from him. it feels like he's not incapable of writing characters with disabilities on the whole, and i do think there are cases where he's gotten better at it. i know many people might feel differently about kizuna's feelings relating to becoming wheelchair-bound, but i personally sympathize with her because a big dream in her life was to become a dancer and i also experienced a major disabling life event that limited my autonomy at a similar age and felt similar ways. this doesn't let aini off the hook, though, because everything that happens with gen is bad.
however, even if it's gotten better, i think that (like i said in the first post) even the non-evil characters only experience their disabilities when it's plot relevant. ryuki's psychosis mostly exists to create an unreliable narrator timeline twist. snake can utilize his artificial hand to slip his bracelet off (which he never experiences drawbacks from past that single scene, by the way!). sigma's white blood (while admittedly funny) is the only way he ever really experiences a difference with his arms literally being both prosthetics.
with the repeat occurence of this type of writing, it kind of feels like he doesn't really conceptualize disabilities as something people actually live with and that representing them in certain ways might make his audience feel uncomfortable or upset. it feels more like he thinks about them as a vehicle to deliver a narrative instead of something that some people just have. i didn't mean to make this post so long but honestly this is a feeling i've been trying to articulate for a really long time so i hope it makes sense.