YMMV / Marie D. Suesse And The Mystery New Pirate Age!
Broken Base: The Lemony Narrator attracts a small amount of controversy. Some people enjoy it, but a few are turned off by it and/or disagree with some of the observations.
Fridge Brilliance: Similar to what one reviewer pointed out, Mar, by eating the Logic-Logic fruit, thus forfeits the chance to eat any other one, and with it, the opportunity to become a competent fighter, much less Mary Sue.
In the second chapter, it is mentioned in passing that Mar resented that her mother often felt as though she wasn't living up to her expectations. In Chapter 32, it's revealed that Mar's mother was taken in by a woman who essentially helped reform her by being strict with her, and resolves to make sure that Mar isn't spoiled like she was.
The Weapon Tombstones provide several: one doesn't have a weapon, because the stones were clearly looted, and Sanji fought with his feet. Chapter 22 also shows their burials, with Usopp working on memorials the reader already knows will be destroyed.
Jerkass Woobie: Monkey D. Madelyn can be seen as one; one reviewer pointed out that for everything she did, she's the end result of a badly written Mary Sue who wants to fulfill her dreams, an assessment the author agreed with, as does Mar by the time that she learns that Madelyn is her mother.
Phalanx: That is indeed one of the main themes of the story neatly summarised. I wanted this to be a more realistic and accurate reflection of what causes a Mary Sue instead of a usual bash-fic, and no, I don't believe that most of them are created to be deliberately malicious in nature. I honestly think most of them mean well but just really don't know any better. As another reader noted, the road to hell is paved with good intentions.
Moral Event Horizon: Monkey D. Madelyn crossed it when she manipulated events to get Luffy captured and executed, getting a large portion of his rescue party killed as well, all because she thought taking her brother out of the race to become Pirate King would make Law happy. Granted, she did so under the assumption that Luffy's crew would succeed in rescuing him, albeit being delayed long enough for only Law and Kid to have a shot at finding One Piece and was horrified when things did not turn out as she had anticipated.
St. Magnus the Tenryuubito probably crossed it many times over, but reading about his hobby of throwing people into tanks of piranhas and sharks just emphasizes just how twisted he is.
Relationship Sue: The main antagonist, Monkey D. Madelyn, seems to have this as her power.
Phalanx: "this story is in some ways a modern-day version of a dark fairy tale and it is in keeping with the tone of those kind of stories. They weren't particularly subtle about their aesops. If you're familiar with TV Tropes, there's one that goes 'Some Anvils Need to be Dropped'. I think this fic drops whole hailstorm of them."
Stoic Woobie: Most of the main cast, with the exception of the Mar and Mr. Suesse, are this.