I liked the overall plot well enough, and I thought the general execution of most of the show's ideas (PK in general, queerats, Fiends) was done well. The show does a good job of making the viewer question which side is the "villain". There was good character development for Saki and Satoru but very little for anyone else - this is redeemed somewhat by how interesting Squealer, Kiroumaru, and Tomiko (the old lady) are. The soundtrack was gorgeous and contributed well to the show's overwhelming atmosphere. No other show has consistently made me feel such a sense of unease with just about every episode. The animation was patchy here and there but the art was beautiful when it needed to be, so that's a minor gripe.
Actually, most of my gripes are minor, but there are a lot of them. I'm disappointed by many small plot holes, particularly regarding use of PK in many scenarios - why don't characters fly more often, for example? Why didn't Saki blow away the bioweapon from Satoru when confronting the Fiend, or use her own PK to pull him toward her? Why can't a normal PK user just go ahead and kill a Fiend and then die to death feedback?
Regarding the last point, I understand that death feedback starts acting even upon thoughts of hurting another human, but its effects (inhibition of the liver and parathyroid) should take at least a few seconds to kick in, whereas killing another human should be instant. The only explanation that I've found even slightly convincing is that years of education, conditioning, and hypnosis have paralyzed most of the public from doing this, but this begs the question as to why a society so paranoid of Fiends doesn't come up with a more reliable countermeasure, or why the geneticists who engineered the changes to the human genome didn't think to include some kind of "failsafe" for this exact event. Death feedback also appears to be entirely mental (we don't see it affect Saki early on in a flashback until the elder makes her aware that she's hurting him). In that case, it should also be possible to hypnotize someone else into killing a human, or to use myriad other techniques involving PK to circumvent death feedback, at least temporarily.
In general I also found SSY's use of flashbacks to be heavyhanded more often than not, especially after the first arc. When it's not infodumping, SSY generally seems to support the "show, don't tell" mentality, but frequently replays a flashback when it really doesn't need to, seemingly spoonfeeding the viewer "Hey, look, this is a callback to two episodes ago". Perhaps this is a more noticeable fault if you binge watch like I did, but it happened enough that it started to really get on my nerves by the halfway point of the show. Reminding the viewer about a previous scene is perfectly fine if it's done naturally, but not when you copy-paste that scene in with a gray filter - and certainly not when you do that dozens of times over 25 episodes.
It also feels like SSY becomes a totally different show during several points and ends up dropping many minor plot points or themes. This is done well in some parts; the transition from the Squealer/Kiroumaru war to the festival massacre to the hospital scene was excellent, for example - but it falls flat in many other areas. One instance is how human sexuality is a major theme toward the end of the first arc and the beginning of the second arc, but is never touched on again after Shun dies. The queerat war has little purpose other than to introduce Squealer as a character and to introduce us to the structure of queerat society - something that's necessary but doesn't require as much dedicated screentime as it had. We also see Satoru violently killing hundreds of queerats as a child and going too far, then never revisit this again in the second and third arcs.
It feels like SSY juggles a lot of balls in the air and decides to drop some of them while throwing new ones up there. I really liked the show best when it was entertaining multiple plot points at the same time. I found the flashbacks in episodes 1, 2, and 3 all extremely interesting and very effective at keeping the viewer invested in the show, culminating in episode 4 when the false minoshiro explains basically everything, in probably my favorite infodump of all time. Afterwards the show honestly struggles to balance "setup" and "payoff", if that makes sense, sometimes introducing concepts in one episode that would be mentioned for the first time in the next episode at best, and would be completely irrelevant for the next dozen episodes at worst.
Normally these would be minor complaints if they only came up, but most of these critiques that I have popped up over and over again in my head, particularly during the latter half of the series to a degree where it was preventing me from fully enjoying the show. It certainly did a lot of things extremely well, but it absolutely falls short of a masterpiece for the time being. Psycho-Pass is a thematically similar show but was magnitudes better at its execution, in my opinion. SSY is currently sitting at somewhere around a 7.5/10 for me, and I'd appreciate it if someone could clear up some of my concerns, because I really wanted to love this show.