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.
YMMV: Yakitate Japan
Arc Fatigue: The Yakitate 25 arc starts off decent enough, with some surprising plot points (like Azuma losing for the first time in the series,) but quickly falls into a strict formula so bad that the reader can actually start to predict how every single match will play out, right down to the basis of the gags.
Complete Monster - While Yukino's done any number of truly monstrous things (up to and including murder just to ensure her Karma Houdini), the one that probably has the most impact for the reader, and certainly the characters, is when she steals Tsukino's mother's ashes and flings them around at a withered dead tree, cackling with glee and shouting insults while a very young Tsukino sobs and begs her to stop. The series picks few bones about the fact that she's a literal psychopath who only finds joy in the suffering of others.
Esoteric Happy Ending: Parodied and lampshaded repeatedly in the Yakitate 25 arc, where Azuma declares any victory a happy ending, ignoring the fact that most of his opponents have shape-shifted with no sign of changing back any time soon, and the occasional bad thing that happens to some other character (like Ken becoming a yazuka leader against his will, or Kuroyanagi suffering severe internal bleeding as a result of a reaction.)
Evil Is Sexy: As the manga goes on, Yukino wears less and less the more you learn of her evil. Culminating in chapters where she wears nothing at all.
One example: She is somehow able to wear this getup to a public playground and not get arrested.
Harsher in Hindsight: The last two chapters has, due to usual Yakitate craziness, someone turning into a country, forcing Kawachi to eat bread to have a reaction to save the day, because a sudden new giant land mass displaces water and has sent a tidal wave towards Japan...
Ho Yay: Ken-chan & Mokoyama, Kanmuri & Kuroyanagi-sempai.
Moral Event Horizon: Yuuichi Kirisaki returned home to his starving and dying kids while they were respectively 10 and 5 to eat a large bread right in front of them and denying them to eat any of it, all the while commenting on how delicious it was.
Woolseyism: The English translation of the manga does a pretty good job of translating the Japanese puns into English ones.
The Indonesian Translations on the other hand use a rather interesting way where the joke is kept and added a translator note. As a bonus, there are several reference to Indonesian culture that is added by the translator.