I personally don't have that big of a issue with Saix's atonement. I wish we could have seen more of it and his thought process. Maybe in the novels or manga hopefully? That being said I kinda get why some are split on it. We never truly see how he reaches this point of clarity and wanting to make up for how he acted. Saix was basically the main antagonist of Days on a personal level, even more then Xemnas, and he was pretty loathsome in KH2 as well with his treatment of Sora and willing to attack Kairi and Namine. I consider Saix one of the better Organization members in terms of character and backstory.I don't think Saïx not explicitly talking about his betrayal of the Organization to atone was a failure of the writing.
First, I like how his betrayal is hinted at in the game ( I love the shot of Roxas pointing his Keyblade towards Xemnas and Saïx when he says 'and others too') and then Vexen's Secret Report allows you to work it out for sure but it never straight out tells you so it's something you can work out.
Secondly, I think him not admitting that he was helping Axel and preferring to play the part of an enemy until his defeat makes sense for him. He's a very reserved guy, which you can see even when he's a kid in BBS, so I can see him finding being honest about his personal feelings harder than pretending to be the cold, cruel person he became in the original Organisation.
I do feel maybe something could have been added in Re Mind to show his true intentions more clearly and am not defending tacking Subject X onto his and Axel's backstory though.
Unfortunately Saix's atonement comes at a price. Because of it, Lea/Axel is rendered useless in KH3 as Saix saved both his friends with no involvement from Axel whatsoever. It makes Axel's promise to save Roxas pointless and his seeing Xion in Kairi equally pointless and goes nowhere. It also makes Lea having a Keyblade pointless outside popularity. It should have been joint between them if you wanna go that route. Have Saix secretlty deliver the Roxas vessel to the heroes early and Axel plays a role in sparking him, thus keeping his promise. And when Axel and Saix have their clocktower meeting, have Saix keep subtlety nudging Axel about the third ice cream until he remembers there's someone else he has to save. Keyblade Graveyard Axel realizes Xion's the third ice cream and helps restore her. This way you have Saix still play part of his secret atonement but Axel also keeps his promise to bring his friends back.
And finally the conclusion. I loved seeing Isa join the group, and I may have said this in another thread, but personally I thought it happened a little too soon. I would have waited, let RAX begin a search for Isa in a post KH3 game, similar to looking for Riku. This way we can see Isa bond with Roxas and Xion and so when he does join everyone in Twilight Town it will feel truly earned. The Twilight Town gang all sitting together eating ice cream was beautiful one of my all time favorite KH moments, but it was done too early. The end goal should have always been them sitting together with ice cream in hand, but if there had been one more game before it, I'd say it was 100% perfect.
But that's just my take on the whole Saix/Isa thing. Sorry for all this Dast, lol.