Accidentally-Correct Writing: The assault rifle that Shadow pumps in the opening cinematic is believed to be a Troy 223◊, a pump-action rifle that looks like an assault rifle, which wouldn't enter production until 2014, nine years after the game's initial launch. In reality, though, the sequence was decided early on and the studio referenced a toy gun that did exactly what was shown.
Blooper: In a scene before Space Gadget and Lost Impact, Sonic says "We're on our way to the ARK, so I guess that means we're going too!" Presumably, this line should say "They're [the Black Arms are] on their way to the ARK, so I guess that means we're going too!", unless the first "we" referred to himself and whomever was in the spaceship, and the second "we" referred to the group plus Shadow.
Sega is really not fond of referencing this game, with it mostly getting passing mentions in supplementary material. Only three games, Sonic Rivals, Sonic Chronicles and Sonic Frontiers, reference the events of the game, but the first two were made around the same time (2008) and in the west, and Frontiers only mentions the Black Arms in optional message logs. That said, Sega appears to hold the soundtrack in nice regard, with a remix of Westopolis and the menu select theme appearing in Sonic Forces and the main theme being played as part of the Sonic 30th Anniversary concert. With the announcement of Sonic X Shadow Generations and it having a focus on Shadow's past (especially with Black Doom playing a major part), Sega seems to have finally started embracing this game again.
Archie Comics was not allowed to make an adaptation of the game and barely allowed any stories featuring the Black Arms. Some of them showed up in Sonic Universe post-Cosmic Retcon headed by a new leader named Black Death, who was instantly killed off in the same story that introduced him. But Sega wouldn't let Black Doom be used in any capacity, with him only showing up in one flashback panel. The Archie continuity would later gain Eclipse the Darkling, a new Black Arms creation who skewed closer to the usual anthro Sonic design, which Sega likely only allowed because of that compromise. (Coincidentally, Ian Flynn's podcast revealed that Eclipse also served as a replacement for Mephiles the Dark, who was meant to appear in the "Shadow Fall" arc before being written out at Sega's request.) Though if we believe some statements, an adaptation was on the table when Ken Penders was writing, but he was given very little information beyond some screenshots, which was nowhere near enough to work with; as soon as it became clear it wasn't going to work, an original story arc with Shadow as the main character was done as a compromise. By the time there was enough information for a proper adaptation, the game was already considered outdated.
Daniel Rice, the Blur Studio artist who created this poster depicting Shadow looming over an injured Sonic for E3 2005, has expressed distaste not only towards the game's use of firearms (which Blur Studio themselves evidently tried to talk Sega out of), but also confusion towards why Sega would desire to promote the game through upstaging their series' mascot and main character.
Creator Killer: This is the last platforming Sonic game to involve Yuji Naka, who departed Sega a few months after the game hit store shelves. Both it and Sonic the Hedgehog (2006) worsened the issues confronting Sonic, and Naka has remained in the background in his career since.
Executive Meddling: The reason for the English Dub cast since Sonic Adventure being replaced with the cast of Sonic X was caused by Sega of Japan demanding that the games and anime have the same cast.
Follow the Leader: The primary reason Shadow the Hedgehog exists is because of the changing landscape of video games in the era it debuted in. The Sixth Generation of Console Video Games saw shooters on console explode in popularity between games like Halo: Combat Evolved, Grand Theft Auto III, and the first Call of Duty. Shifting demographics also meant gamers had largely turned against the mascot platformers of the 90s, demanding more "mature" games (often with guns) over brightly colored, lighthearted affairs. Sega even got letters outright asking them to let Sonic shoot things in his games. They were naturally hesitant to give their mascot a gun, and compromised by letting his rival use one. Ultimately, the game received mixed reviews as some fans found the game utterly hilarious, though it did sell pretty well.
New Work, Recycled Graphics: The in-game models of most of the characters sans Rouge (who returns to her Adventure 2 outfit) are recycled from Sonic Heroes.
Orphaned Reference: In the endings, Shadow states "This is WHO I AM!" The main theme of the game was originally "Who I Am" by Magna-Fi. (Though it can be argued the line still works, at least partially, with "I Am... All of Me" by Crush 40, the song that replaced "Who I Am" in the final release.)
The Other Darrin: None of the original San Diego-based voice actors from the games reprised their roles, as the dub used the New York City cast from the 4Kids Entertainment dub of Sonic X. In the case of Dr. Eggman's voice actor, Deem Bristow, it was impossible.
Pop-Culture Urban Legends: Fans will often cite that the Japanese version of the game is uncensored, complete with Maria's original death scene in the intro and enemies spewing red blood. That isn't true; Japan received the same version other countries did. At most, there are signs that the game was censored before release due to some lip flaps in the CGI cutscenes not quite matching what the characters said, but even then, an "uncensored" version was never released anywhere.
Role Reprise: The 4Kids Entertainment cast voicing the characters in this one counts as both this and The Other Darrin, since while said cast replaced the previous games' voice cast, they had voiced the roles in the Sonic X dub.
First and foremost, the game was going to be even edgier. Sega wanted the game to be one age rating up from previous Sonic games, which at the time development started was T for Teen. However, when the ESRB introduced the Everyone 10+ rating between Everyone and Teen, Sega toned down the game to fit the new rating. The changes made as a result of this included:
The original T-rated version of the game would have shown Maria's death in the opening, rather than cut away as the player hears the gunshot. The final game does show a monochrome still image of Maria getting shot just before the Heavy Dog boss fight. The same image appears in color on her card in Sonic Rivals.
Early trailers showed enemy Black Arms spewing red blood when hit. In the final game, their blood is green. Of course, the aliens themselves are still reddish, not to mention the similarity of our titular hero's red blood to his otherworldly creators.
There was a lot more swearing, including Shadow saying "Just what the hell was that all about?" in the opening cutscenenote changed to "Just what was that all about?" in the final version, but the lip-sync is still for the original line and Sonic saying "I'd hate to piss off G.U.N."note changed to "I'd hate to tick off G.U.N." in the final version, although Jason Griffith claims he doesn't remember recording the latter. In the final game, Sonic only swears once.
Sonic: Damn, they got away! Leave it to me, I'll chase 'em down!
Eggman was also going to be nastier in his levels, and after you had helped Amy you would get to see him attack her before he went for Shadow, with the implication in that boss fight being that Shadow was defending her.
Apparently, Sega got a letter from a young fan saying how cool it'd be for Sonic to have a gun. Sega, wanting to expand their audience, thought it was an all right idea, but thought that the gunplay wouldn't fit Sonic's character, so they gave the role to Shadow.
On a related note, Sonic was supposed to feature in the game's multiplayer mode, but was cut very early due to Sega management's qualms about their heroic mascot using guns.
Magna-Fi's "Who I Am" was meant to be used as the main theme of the game, but it was switched out with Crush 40's songs due to Executive Meddling by the band's manager, who instead wanted the song on one of their albums. Magna-Fi would be able to still contribute to the game with "All Hail Shadow" as the True Hero theme.
"Broken" and "All of Me" (no relation to the Crush 40 song), both performed by Sins of a Divine Mother, were meant to be used in the main game. Both were cut and "Chosen One" by A2/Mona Lisa Overdrive (which has some overlapping members with Sins) was made as consolation due to Sega being unable to contact the lead singer in time for permission.
Writer Conflicts with Canon: The Pure Heroic Path being the canon route, according to Word of God from Sega, doesn't align with the Last Story. For starters, the Last Story implies multiple events from other routes happened, which is impossible in the Pure Heroic Path. According to a fan, it's more likely the "Together with Maria" path (Neutral-Neutral-Dark-Hero-Hero-Dark) is the correct path.
Several interesting paths can be taken — including the all-Chaotix paths, a path in which you help out Eggman three times, a path in which you can beat Knuckles down three times, and numerous paths involving visiting Black Doom's flying temple twice, both to activate it and to destroy it.
If you help Rouge, it is impossible to help Amy.
The investigation of the Chaotix is very important in The Last Way, and there are only three ways to do it. Two of them don't involve helping Black Doom at all, and one of those only requires a general selfishness on your part. Some people believe the canon path involves helping them gather their data. This seems to give the best continuity of all the paths.
In the level Iron Jungle, take a look at the Shadow Androids in the opening animatic. They have a lower polygon count than the real Shadow, making them look cruder and more angular. Their colour is also a different, slightly duller tone.
This is the first game in which Shadow used Chaos Blast, despite him being in threeothergames before it, and he has only used it very rarely since.
This is the final platforming Sonic game to be supervised by Yuji Naka, who was the one remaining member of the power trio that created Sonic. He left during development of the next game, Sonic the Hedgehog (2006), but also took a considerable chunk of Sonic Team's staff with him, which ultimately helped undermine Sonic '06's development and led to one of the most infamous missteps in the video game and entertainment world. Whoever succeeded Naka ultimately was demoted/fired at the end of the decade and replaced with Sonic the Hedgehog 3 level designer Takashi Iizuka.
◊, a pump-action rifle that looks like an assault rifle, which wouldn't enter production until 2014, nine years after the game's initial launch. In reality, though, the sequence was decided early on
