Season 3 started strong but they messed up. They hinged too much on Lena Olin returning as SpyMommy and never figured out how to make the story without her.
They should have kept Allison longer and let her be Julian Sark's evil girlfriend/partner. Killing her off to replace her with Lauren was dumb, misogynistic (because of course, Sydney's romantic rival can't just be the wronged person in the triangle, she has to be an evil slut who never loved Vaughn), and borderline racist.
Sark's billionaire father and Russian inheritance plot was ridiculous and clearly just do to fans wanting more from a character that worked better as a two-dimensional villain.
We should have explored Sydney's missing years and her trauma from it better. Instead of whitewashing Sydney where her alter ego was another superhero, Julia Thorne should have been a broken tool who committed evil actions. And since they wanted SpyMommy back so badly, we could have tied her rescue and recovery to her while keeping her behind the scenes.
Nadia's story was a last minute addition and it showed. (Although I think they played with the idea of Sark being Sydney's lost sibling, a twin because of JJ's obsession with all things Star Wars). If they had planned the season better (see my first point), they should have introduced clues about her earlier, and even introduced the character earlier in the season without revealing who she was. She also could have been tied into the mystery of Sydney's missing years.
Rambaldi made less and less sense each season. JJ should have decided what he wanted the Endgame to be and worked the mytharc accordingly. Because he kept playing a guessing game with the audience until the very end, there are just too many holes in the plot. This is a problem for the series overall, but it's worse in season 3 which really leans hard into the mythlore.