Shu Takumi originally wanted the Ace Attorney series to end with Phoenix Wright: Ace Attorney - Trials and Tribulations, as he felt that main character Phoenix Wright had been fully explored and had no reason to continue, stating:


When it was decided that a fourth game would be made, Takumi wanted the game to have a new main character and story, witho Phoenix originally not planned to appear. However, his colleagues wanted Phoenix in the game in some form, which ultimately led to him being the defendant in the game's first case, "Turnabout Trump".

According to series creator Shu Takumi in a 2017 interview, Capcom executives issued two mandates affecting the writing of Apollo Justice: Ace Attorney. The first mandate was that the story had to include Phoenix Wright, which went against his original idea for a reset of the series. The second mandate was to incorporate the Lay Judge system, a real-life judicial system, into the story, resulting in the creation of Spoiler:the MASON System game program and the trial run of a new Jurist System in the game's last case "Turnabout Succession". The Ace Attorney series began as a critique of how Japan's legal system handles criminal offenses, but around this time, the system was changing. Japan's legislative body the National Diet gradually implemented a new lay judge system (裁判員, or "Saiban-in") from 2004 to 2009 that resembled more democratic systems in North America and Europe. It calls upon six random common citizens to serve in serious criminal trials as inquisitorial judges sitting alongside three professional judges. Together they make up the judicial panel and actively analyze and investigate evidence presented throughout the trial before ruling on guilt and sentencing. Reflecting this, Spoiler:the Jurist System seen at the end of Turnabout Succession is made up of six random jurors guided by Wright, where the player from the sixth juror's perspective has to rule the defendant Guilty or Not Guilty.

Takumi revealed that as part of the game’s promotion, Capcom collaborated with the Japanese Ministry of Justice and even gave a presentation of the game at the ministry's head office, implying that the system's mandated inclusion in the game was Capcom spreading political propaganda. Despite their cooperation in the government's push for this new system and despite participation experiences being reported as positive and easy to understand, the reception to other aspects of it were largely negative. Complaints included gradually more severe sentencing since its instatement, the risk of criminal penalties for lay judges publicly discussing confidential deliberation details after trials end, and calling upon Japanese citizens to put aside time to participate, who have been increasingly unwilling to do so. This decline in interest has been largely attributed to the length of lay judge trials and even pre-trial proceedings dramatically increasing over the next decade, and due to old age and people simply not being able to make these commitments, more citizens refused to serve or even show up to be vetted for serving in the first place, making it harder to fill out the jury.

The Ace Attorney series has not used Spoiler:the MASON System and the Jurist System since, sticking with the series' traditional Initial Trial system in future games.

The button on Phoenix's hat is the same button worn by Ema Skye in the extra chapter added to the DS port of the first Ace Attorney game.

After Apollo catches Machi Tobaye lying, Lamiroir exclaims "What is wrong, Mr. Justice? Your eyes, they are quite fierce all of a sudden!" despite her being blind.

In the chapter "Turnabout Serenade", inside the Gavinners's dressing room are two references to the UK rock band "The Police". Examining the poster with the police officer on it will trigger a conversation about a band called The Police, and examining the red light on the ceiling will have Trucy talking about turning it on, with Apollo responding with "Don't turn on the red light", referencing the chorus to The Police's hit song, Roxanne.

In case three "Turnabout Serenade", on day 2 in the Wright Anything Agency if you examine the top hat, Apollo will say "That's one of those hats you pull things out of, right?". Trucy will then say "Of course! My hat's like a little universe! Bigger on the inside than on the outside!" which Apollo will reply saying "Hmm... That reminds me of a sci-fi show I used to watch."

This is a reference to the science fiction series Doctor Who and the spaceship the TARDIS which is bigger on the inside than on the outside.