Ass Pull: The infamous rubber bullets twist. Due to the ludicrous amounts of Idiot Ball Majima and Saejima needed to be holding to not notice something was up, the amount of convolutedness and contrivances necessary for the plan to even be pulled off, and the fact that they all still died anyway at Katsuragi's hands anyway, making it seem like its only real purpose was to make Saejima look good. Even dumber is the fact that in real life rubber bullets shot point blank often still kill people anyway, making Katsuragi look like just as much of an idiot. Even Munakata lampshades the absurdity of the plan immediately after the reveal. And it keeps happening through the endgame!
Fans who enjoyed Tanimura's gameplay were torn when he didn't return in the fifth game. Others argue he was the least popular of the three new playable characters and wasn't nearly as interesting as the other two, his story arc had concluded, and his appearance in the game overall was a Celebrity Cameo, supported by the fact that he's also nowhere to be seen in the spin-off Ishin! which brought back several characters who hadn't been seen in the series for a long time. Although Japanese character polls show that he was well-liked in general, and later games do make reference to him, it's unlikely that Tanimura will ever return since his voice actor Hiroki Narimiya retired from acting in 2016 due to allegations of cocaine use.
The truth behind the Ueno Seiwa hit, and that Saejima didn't kill anyone. It completely redeemed him, or it was a shoehorned twist that also robbed him of his badassery or moral complexity.
Contested Sequel: The game is either seen as an improvement to its predecessor or inferior to it. Some fans believed the series would begin to go stale if the series continued to focus solely on Kazuma, and found that introducing more protagonists was a needed breath of fresh air, and enjoyed what they had to offer to the story. On the other hand, the plot of the game was seen by many as a convoluted mess filled with Chronic Back Stabbing Disorder and twists galore, and were torn on how the game's story played out between the four characters, who each have their fans and detractors.
Ensemble Dark Horse: Akiyama's assistant Hana, who's rather popular for being adorable and having Hidden Depths. Fans were disappointed at her lack of appearances in later games aside from the non-canon Dead Souls and her Expy in Ishin!.
Ho Yay: Majima's is intensely devoted to Saejima to the point of enduring serious harm for his sake. For a more concrete example, after Saejima beats him in a boss fight he leans in close to Saejima's face asking for another round. Granted, he's talking about fighting, but this is Majima we're talking about...
Foe Yay: In the final boss fight between Saejima and Kido, it looks like the two opponents are about to kiss while holding their heads.
The plot is kicked off by the fact that Akiyama leaves 100 billion yen in an easily accessible safe in his office. The only security is that the safe requires a button to be opened... which is hidden behind the most prominent book on his shelf. The antagonists of the game found it completely by accident (and the office wasn't even locked).
The entire Ueno Seiwa hit can be considered as one as well. It's absolutely baffling that Katsuragi and Sugiuchi managed to get as far as they could given how easily the plan could have fallen apart at various points had the other parties involved not been holding the Idiot Ball. This was even pointed out by Munakata, who pointed out the numerous flaws in the plan and quickly deduced what was up in a matter of moments.
Memetic Mutation: RUBBER BULLETS Spoilers It's revealed that Saejima actually didn't kill anyone in the Ueno Seiwa hit because his guns were actually filled with rubber riot bullets. Considered one of if not the biggest Ass Pull in Yakuza history, it's become a two-word summary of the goofier aspects of Yakuza 4's story. It's also invoked as a tongue-in-cheek explanation for the more nonsensical aspects of other completely unrelated plots in Yakuza or the surprisingly low canon killcount of the protagonists. Sometimes substituted with other words (e.g. "plastic projectiles" or "elastic munitions", or with "bullets" replaced with other things like "fists" or "helicopters" as appropriate).
For some, the growing number of twists and backstabbings became tiresome by the end.
Saejima's final boss: Takeshi Kido. Not many were buying the idea that he could stand toe-to-toe with Saejima, and thought he should've gone down in a single hit.
The infamous reveal that Saejima shot rubber bullets during the Ueno Seiwa hit, killing no one, due to how much of an Ass Pull it was.
The deaths of Yasuko and Katsuragi. The scene tries to portray her as strong and brave for standing up to Katsuragi after being shot by him, despite her otherwise unintimidating presence, which triggers his sudden Villainous Breakdown when he wasn't even intimidated by Kazuma of all people. There are also those who saw Yasuko's death coming (considering each game so far had an important character die in the climax), and believe her death was the equivalent of being Stuffed into the Fridge just to motivate the male protagonists for the finale.
Narm Charm: How some people feel about the rubber bullets twist. It's such a ludicrous moment in a plot that takes itself very seriously that it ascends to So Bad, It's Good levels.
Rescued from the Scrappy Heap: Some players found themselves instantly hating Taiga Saejima the moment he was introduced as a mass murderer in the Ueno Seiwa hit. But once he fought in the Underground Coliseum and shot back at the audience tearfully denouncing the horrors of killing, not only did he redeem himself in the eyes of the same players who hated him, they also considered it his Moment of Awesome. If that wasn't enough, it was later revealed that he actually didn't kill a single person since all guns were loaded with rubber bullets.