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.
Accidental Aesop: Don't use your daughter as a pawn in a criminal scheme. In addition to the character who did this in Phoenix Wright's trilogy, there are about four characters who do it in Apollo Justice: Ace Attorney. Phoenix Wright had his daughter give Apollo Justice evidence that Phoenix had forged so that Apollo would present it in court; Drew Misham had his daughter forge paintings and evidence for money; Magnifi Gramarye arguably did this when he blackmailed his students with something they had done to his daughter while apparently not doing much to help her; and Zak Gramarye had his daughter help him escape from his murder trial.
Broken Base: Apollo Justice has divided fans into a Phoenix Wright camp and an Apollo Justice camp. Some think the promised fifth game should bring Phoenix back as a lawyer, others believe that Apollo is a good character who just needs another game or two to develop.
And with the confirmation that it will be Phoenix-centric, fans continue to disagree but are being even more verbal about it.
It's also possible to Take a Third Option and enjoy both characters but dislike the time skip and related case. Considering that the Phoenix arc ended on an Earn Your Happy Ending moment, Apollo Justice opens with information that's something of a moodkiller, to put it mildly. It's hard to tell whether people hate Apollo himself, the re-characterized Phoenix, or what the Apollo Justice game itself does to the timeline (which goes way beyond Fanon Discontinuity territory).
With the announcement of Phoenix Wright - Dual Destinies, Capcom themselves seem to have decided to Take a Third Option, with promotional material showing both in the court room.
Captain Obvious Reveal: It's pretty easy to figure out that the amnesiac Lamiroir is actually Thalassa Gramarye due to their identical hairstyles.
Complete Monster: Kristoph Gavin is introduced as a supposedly helpful mentor. He is also the first man responsible for ushering in “The Dark Age Of The Law” by getting Phoenix Wright disbarred. Kristoph ended up taking a massive blow to his ego when a magician and prospective client, Zak, rejected Kristoph as his lawyer. When Zak hired Phoenix instead of him due to a poker game, a furious Kristoph decided to get revenge. He had gotten a shy artist named Vera to unknowingly create fake evidence for the trial, but after Phoenix was hired, Kristoph used the evidence to get him disbarred. Kristoph also manipulated his own brother, prosecutor Klavier, by using him to disbar Phoenix and cheating the honorable Klavier out of a fair trial. Klavier, who knew something wasn't right, was haunted for years. When Zak resurfaced under a new identity years later, Kristoph took the chance to murder him and frame Phoenix. After this, it was revealed Kristoph had poisoned Vera and her father Drew, intending both to die. Vera survived, barely. To pour salt on the wound, Kristoph gloated how Apollo and Phoenix had triggered his plan-their questioning caused Vera to bite her nails- when he had planted the poison as nail polish, knowing her nervous habit. He had even started poisoning her when she was only twelve. After her survival, Kristoph simply enjoyed seeing Vera face conviction for her own father's murder. In the end, he was little but a cruel, petty, selfish man obsessed with glory and destroying those who stood in his way.
Designated Villain: The only reason you go up against Klavier is because he's the prosecutor. Personally, he's pretty much a really nice guy, barring his insults in the courtroom. And calling Apollo "Herr Forehead".
Draco in Leather Pants: Valant Gramarye: Ok, Zak was a jerk; almost definitely more of a jerk than Valant. But that doesn't excuse Valant for deciding to frame him for murder, especially when the main motives were jealousy and money. Try telling that to Valant fans though.
Hilarious in Hindsight: The whole incident about Phoenix Wright getting hit by a car and flung into a pole and only suffered a sprained ankle. With his inclusion in Ultimate Marvel vs. Capcom 3, he had to contend with a variety of attacks, such as She-Hulk's Level 3 Hyper, which involves getting hit by a car (Sunday Driver, according to her), and her new attack in Ultimate swinging a pole. The best part is that the hit and run incident in the game took place on a Sunday.
Idiot Plot: Many people think this about case 4-3, which has all the characters think it's perfectly feasible for a prepubescent boy to use an incredibly powerful revolver without injury, carry a 250lbs man across an arena, and even for the boy to be a secret Interpol agent based on a bit of bloody writing, despite that having been used as a red herring as far back as Phoenix's second case. Even Apollo doesn't dispute the feasibility of the accusations, just that Machi was the one who did it. For this reason, the case is one of two (the other being case 2-3) that are generally considered to be the worst in the whole franchise. Shu Takumi has since admitted to the flaws in the case's storyline, and revealed that he was working on the assumption that Daryan was using his position in the police to manipulate the investigation and throw Machi under the bus for his own crimes, but forgot to make this clear in the dialogue.
Incest Yay Shipping: It would count as Surprise Incest, but some people ship Apollo and Trucy, who are half-siblings. Kristoph and Klavier also have a sizeable amount of shippers, but many times it's portrayed at varying levels of unhealthy most likely because of the following trope.
It's standard for the guilty one to go completely batshit crazy in fury or amazement that their plan has been ruined. However, it gets even scarier with Kristoph, who slams his hand into the desk, his hair flies up as if he's going Super Saiyan, and after that's done, his hair is in a complete mess, his face looks just plain demented, and a psycho-stare that is scarier then even Damon Gant's! That. Is. Scary. And when you win the case, Kristophsnaps. With his hair still a complete mess, he puts a hand to his face, faces the sky, and just laughs. It's clear that he's gone completely insane when faced by the turn of events. He's lost everything by your victory; seven years of planning, gone. And you don't hear anything. You don't hear a sound byte of the laugh, there's no box saying "ha ha ha". No, what there is is a text-based "voice-over" describing the aftermath of the case, and how the killer... laughed, all while you watch his final breakdown in utter silence.
Do NOT perceive Spark Brushel while he's smiling widely.
Player Punch: Mixes with But Thou Must in the flashback trial. Phoenix is blissfully unaware that he's about to present forged evidence, thinking he's riding the easy train to victory. Both the circumstances and the context of the rest of the game already make the player aware this will not end well but they are dragged kicking and screaming into presenting the evidence to move the plot forward. Really makes the player feel like they're responsible for Phoenix's disbarment.
Replacement Scrappy: Apollo, to some. Trucy mixes this with Stop Helping Me! tendencies ("Take that memory, bury it deep down inside you, and never speak of it again"), but your mileage will vary on how long the trope fits.
Rescued from the Scrappy Heap: According to a character poll after the release of Dual Destinies, Apollo is now considered the most popular character. He even beat Edgeworth.
While not outright hated, Klavier Gavin is not as well liked as some of the other prosecutors by the fandom, mostly because of his Designated Villain status removes the antagonistic conflict that made the other prosecutors rivals. Again, how long this trope fits is subjective.
Scrappy Mechanic: The various "scientific investigation" segments were widely regarded as being boring and slowing down the game's story. As a result, the two Investigations games and Dual Destinies dialled it back to only having fingerprinting and luminol testing segments.
Squick: Shut up about your panties! ("Panties!") It's even in-universe Squick for Apollo.
The Woobie: Apollo is either this or a Chew Toy, depending on how funny you think his suffering is.
Vera. Dear god, Vera.
Possibly Trucy as well, if you take some lines from Phoenix at the end of the game into consideration.
Wocky is a Jerkass Woobie, undoubtedly the worst client Apollo gets. In fact he's worse than almost all of Phoenix's defendants because he doesn't come around by the end. But still, almost getting himself killed and all, lied to concerning this, then realising the truth about Alita...He does start to cry at the very end, then abruptly returns to his "gangster" persona before exiting at top speed. It's implied he understands what his father has done for him and that the family will be okay.
Klavier. Poor guy has to prosecute his bandmate and later his own brother.