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.
Classic Tails randomly shows up out of nowhere without any explanation after you finish the battle after Death Egg Robot/Big Arm. Of course, it's explained from Word of God that they were unable to make a cutscene with Classic Tails' first appearance, due to time constraints.
Blaze, who lives in Another Dimension, somehow came over to Sonic's dimension for his birthday without any explanation. No one questions this, either.
Author's Saving Throw: The finale of the game established once and for all, in-canon, that Dr. Eggman's real name is still Dr. Ivo Robotnik, intended to curb the fandom debates about which of them was his real name or not. The good doctor humorously notes this when addressed as his real name by Tails, saying "Nobody calls me that anymore."
Broken Base: The entire game itself can qualify with fans claiming that its a good game despite its obvious lack of a plot, while others claim that the lack of one really drags it down. That said, in a rarity for Sonic fans, the general consensus is that the game itself is solid, with its only glaring flaw being the plot.(Or lack therof)
Disappointing Last Level: The Final Boss fight in the HD version has received its share of criticism, with the primary complaints centering around the visual design being very confusing and overall vagueness about how to beat it.
This isn't limited to the final boss. The last part of the game has levels that take a huge spike in difficulty, and both Classic and Modern Sonic have to drag themselves through really long levels at the end.
Whereas most levels are actually expanded upon, making them more grand and interesting, it can be said that Planet Wisp (the last proper level before the final boss) suffers from the opposite. Wherein Sonic Colors most stages had two to three different Wisp powers on average, each stage (Classic or Modern) only uses a single Wisp power-up. If that's not bad enough, the levels are also some of the longest in the game, making sure to overuse the gimmick Wisp power well before you reach the end.
One YouTube reviewer even went so far as to call Game Informer out on their biased opinions in the middle of his own review.
While IGN's review gave the game a fairly good score otherwise, the reviewer going out of his way to pan the music accompanying Modern Sonic's stages and questioning those who do like it caused a significant amount of backlash regardless.
There are several others which are mostly context specific. For example, Classic's Flame Shield skill neuters almost every obstacle and enemy in his Crisis City level aside from bottomless pits, and the jump dash you get from it has ridiculous range. Classic's Homing Attack is also pretty intense because it removes the challenge in trying to aim for an enemy to bounce on to reach higher places.
The Homing Attack does have one obvious drawback, though: you don't obtain the same forward momentum you would by doing a regular Spin Jump. Relying on Homing Attack might result in you missing a higher route due to not having enough air.
Right at the end of the credits, the 20th Anniversary badge comes up, and the voice of a crowd of people yells "Happy Birthday, Sonic!". The voices? It is the voice of the fans; it's a combination of 2 recordings from the Sonic Boom and Summer of Sonic events from the same year!
The Japan-exclusive pre-order compilation CDs for the game are titled "History of the First Stage" (White Edition for the PS360 version, Blue Edition for the 3DS). Guess what the level selection for the 3DS version primarily consists of.
Shadow being fought in Radical Highway instead of outside Space Colony ARK in the 3DS version of the game suddenly makes a whole lot more sense once you remember that, instead of referencing the final boss of the Hero side of Sonic Adventure 2, recreates that game's intro movie instead (an Offscreen Moment of Awesome until now). That, alongside technical limitations and the fact that Radical Highway is also the level where you play as Shadow for the first time in the entire series, completely justifies the trope.
Hollywood Pudgy: In-universe, Knuckles asks the Classic Sonic if he gained weight. This causes Classic Sonic to sadly rub his round stomach.
Hype Backlash: On its release date, it was largely considered the greatest 3D Sonic game ever. While the backlash is not as significant as say, Colors, or Adventure 2, the praise for the game has waned somewhat over the years due to such factors as being too short, having no real plot, and/or being too much of a nostalgia trip.
Tony Harnell announced back in February 2011 a new version of "Escape from the City" was made. A couple months later, it's used for Modern Sonic's City Escape.
Classic Dr. Eggman teams up with Modern Dr. Eggman. Further, Classic Tails calls him Dr. Robotnik, but he says that nobody uses that name anymore.
It's Short, so It Sucks : The game cuts out the Padding that even Sonic Colors had (the "remixed" short level sections were relegated to mostly optional challenges), but the game still receives a bit of critique for its shortness.
It Was His Sled: Several people were able to guess that Classic Eggman was in the game days after the game was announced.
It's often joked or speculated that the Time Eater is the personification of the SonicFanbase.
It was also joked that Time Eater's true identity was the infamous barrel platform from Sonic 3. A trap that is very well known for eating up time.
A joke that spawned from Modern Sonic's final line ("Enjoy your future, it's going to be great!") is to accompany it with any variant of Modern Sonic warning his past self afterwards that 2004, 2006, and 2008 are going to be rough years, or a Gilligan Cut of Classic Sonic going through said rough years.
↑ & ↓ & ↻ (The music for Speed Highway includes the repeating line "Up and down and all around;" the meme itself coming from the original Speed Highway from Sonic Adventure.)
Most Annoying Sound: "Time for a CHANGE of PACE!" Eggman will say this damn phrase constantly in the Egg Dragoon boss battle. Grinding on the rails so you can get to Eggman? Pace change. Getting OFF the rails? Thou pace hath changed. Spawns the wall-jumping part of the sidescroll fight? Change of pace.
Sonic's friends during the Time Eater battle. The worst part probably being that, while they talk constantly, none of them seem to think it'd be smart to say something helpful until the last attack on the boss, which is the only part that tells you what to do anyway. So while you're sitting there pressing buttons to figure out what they do, they're all standing there telling you that "It looks like a homing shot!" over and over and over again.
Polished Port: The PC version, which reduced the loading times significantly.
Unfortunately, the PC version does not have the ability to play the original Sonic the Hedgehog.
Taken Up to Eleven with the uncovering of the half-broken remains of the graphics rendering engine of Sonic Unleashed during the creation of the Generations Unleashed game mod. After fixing it up, it enabled a lot of extra features that were disabled in all versions of the vanilla game, such as directional shadows, light shafts, more dramatic lighting effects and a more advanced speed blur system. On top of that, thanks to it's unfinished nature disabling certain functions, it actually gives the game a significant boost in FPS. The difference that the rendering engine makes, especially in stages like Sky Sanctuary, Speed Highway and Seaside Hill, is absolutely jaw dropping. Unfortunately the renderer doesn't work with weaker graphics cards, instead causing the game to look as if you were playing it with a thick layer of Vaseline on the camera.
Rescued from the Scrappy Heap: Silver the Hedgehog. He goes from being one of the cheapest and most aggravating boss fights in the series back in his debut, to this game, where he gets a very enjoyable rival boss fight with a considerable amount of HSQ. Basically, what Sonic '06 did for Shadow, Sonic Generations did for Silver.
Crisis City. While it was certainly one of the more acclaimed stages in Sonic the Hedgehog (2006), it's definitely a LOT more fun in this game. The physics and engine in the Modern stage are far superior to the original, and it even provides some fantastic level design in its Classic stage.
Scrappy Mechanic: Black holes, during versus matches in the 3DS version. There's a reason this is the only instance this gameplay gimmick appears.
The same can not be said of the rest of the cast in the final battle. It most certainly does not help that the final battle is also That One Boss.
Voice #1: It looks like a homing shot!
Voice #2: Be careful Sonic!
What makes them even more annoying is that, the one hint you really need, namely "aim at the core and boost" gets drowned out by a dozen repetitions of "that looks like a homing shot".
Equally useless is the final instruction, which if misinterpreted will be played over and over for eternity:
Tails: Sonic! Press L1 and R1 at the same time to combine your powers! ("And hold them" would have been useful 20 minutes ago, Tails.)
Tainted by the Preview: After the level list was leaked, some fans were disappointed by the lack of variety between them. At least, until it was shown that some levels will be radically different from the originals. Takashi Iizuka saying that the 3DS version will ignore levels from the Game Gearspinoffs didn't help much either.
The reveals of Shadow and Silver as boss battles. Then it turned out that both Rival battles were incredibly fun to play, and have been a considerable boon to the popularity of the characters ever since, particularly Silver's.
The Death Egg Robot has been subject to claims of It's Easy, so It Sucks, though it is the first* arguably second, if one counts the Metal Sonic rival battle as a complete boss fight proper boss in the game. Big Arm also was subject to this, also having been nerfed from its Sonic 3 appearance.
That One Boss: The Time Eater. Awkward controls, lack of clarity on what exactly to do, a cluttered screen, the standard ring-draining mechanic as the rest of the series, and Sonic's friends never shutting up. On the other hand, the battle on the 3DS version is much easier.
Planet Wisp Act 1 is also this for many people, for a combination of its incredible length and the clunky mechanics of the Pink Spike Wisp. Not the best of combinations. Act 2 also gets this, but not quite as badly, as the Orange Rocket Wisp is devoid of any control issues the former has.
They Wasted a Perfectly Good Plot: Many fans feel the plot was too thin, the linking between events could have been done better, and had many missed opportunities regarding character interaction and more nudges or references to previous games in the series. This is especially true after the twoprevious anniversary games had far more engaging plots. Although the latter is generally considered not very good either, but this is the YMMV tab.
Villain Decay: Subverted: Eggman is once again overpowered by the Monster of the Week, two times, after the Death Egg Robot boss and the Egg Dragoon boss, but only after his defeats at Sonic's hands have left him vulnerable. And then it's revealed prior to the final boss that Eggman discovered the Time Eater after the events of Sonic Colors and teamed up with his past self to tame it, leading to the Eggmen putting the events of the game in motion.