These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Attempting to execute Noel, Rise and Makoto, only saved by Akihiko and Noel's transformation into Mu. Likewise, their declaration that they really aren't the La Résistance people think to oppose NOL's totalitarianism, they're just using it as a propaganda to get more members and then fulfill their selfish ambitions.
And while she was a traitor, their treatment and planned execution for Litchi was far too harsh. Especially since she spilled no S7 secrets to NOL or Orient Town.
Rescued from the Scrappy Heap: Philemon is doing his best to aid the heroes, after what happened in Persona 2, and is generally much more reasonable. He wasn't as much of The Scrappy back in the games, but this development pretty much made him look less of an ass that is suspectible from being called a Jerkass God.
The Woobie: Being based on two Woobie-licious series, this fic keeps it going.
Taokaka. Oh, poor, precious Taokaka, turned from innocent idiot to regretful, scared child by Nyarlathotep. Luckily, she gets better.
Iron Woobie: Mitsuru, given her endless torture at the hands of Relius.
Then there's Litchi... where her decision to join NOL came to bite her in the ass so hard. Sector Seven's decision to execute her and poison the whole Orient Town for punishment, Kokonoe AND Linhua condemning her, and then there's the encounter with her Shadow, who accuses her for being nothing more than an obsessed bitch... all because of that. Her 'Iron' status is starting to crack as even if she's trying to keep a calm mind, there were times she utterly broke down.