When Modern Sonic and Tails comment on Green Hill Zone, Tails, of course, doesn't recognize the first level. Because it was the first stage of the the first Sonic the Hedgehog, and Tails wasn't even introduced until Sonic 2, so he never got to see this.
What makes this make even MORE sense is that Tails remembers the smell from Chemical Plant Zone, once again BECAUSE HE'S FROM THE SECOND GAME. Not to mention all the times you have to submerge yourself in the chemicals, poor Tails is probably sick of it all.
In Speed Highway from Sonic Generations, play close attention to the rocket. In Classic Sonic's act, he grabs an idle rocket to enter a dimly-lit, empty shopping mall-esque area (the one from the Goin' Down section in Modern Sonic's act). The rocket flies through the building's windows, but we never see it crash. In Modern Sonic's act, he just happens to be passing by the still-flying rocket after the second 2D section, grabbing it to get to the highway with the cars — and the rocket finally crashes after he lets go of it. — The Dead Skin
The boss battles in Sonic Generations suddenly make some sense to me. There's a reason they take place between certain levels; they coincide with time-travel. Sonic the Hedgehog CD was set between Sonic 3 & Knuckles and Sonic Adventure, and its plot was based on time travel. The first Boss Battle is between the levels from those two games. Sonic the Hedgehog (2006) had a time-travel plot (one which erased its own events) and the Perfect Chaos boss battle was between it and Sonic Heroes. And The Egg Dragoon is after Sonic Colors because that was Sonic's most recent victory before being taken into White Space himself. Every time the Time Eater went through time, and a time-travel based event happened, there's a boss battle between the levels.
However, this doesn't explain why none of the boss battles have to do with those games with time-travel plots.
Because it's not the boss battles. Observe the rival battles and the stages they take place in. The first boss battle is against Metal Sonic, and takes place on the Stardust Speedway. The final third of the game has Sonic facing Silver in Crisis City (Shadow is sadly inexplicable). There's no avoiding these battles either- it could be that these fit the aforementioned theory regarding time travel.
This game may form a Stable Time Loop with Sonic Colors in terms of the Wisps: Sonic here has already used them, and does so during the level, using Wisp Capsules. Given that the tractor beam is still active, we can presume that this happens before the events of Colors. The Wisps, however, are new to this, and realize the significance of this, which is why the Cyan Wisp flies into Sonic on meeting him, and why Sonic & Tails are swarmed by several Wisps in the 2010 game.
So think about the game as a whole for a second. So what are you trying to do? You're trying to restore the world in all times to what it was once. Which levels are comparatively easy to restore? The ones of the Classic Era, still mostly beloved by the fanbase. When does the first major difficulty spike happen? Crisis City, a level which is from a game that is nearly universally agreed upon to be horrible and which would be very hard to redeem in the eyes of the fansnote They did. Which characters appear later, and as such are harder to restore? Most of the characters introduced later on, who would definitely need more effort to redeem than, say, Tails or Knuckles. What happened to the world in the first place? It had all the color sucked out of it. The whole game is a symbolic reconstruction and redemption of the franchise from its lowest point.
Furthering the point, the final level, Planet Wisp, is an extremely long slog in both acts. The character who is rescued after completing it? Charmy Bee, one of the least-liked characters in the franchise. It makes sense that he would take the most effort to redeem out of all the characters.
Why does Classic Sonic have the Homing Attack as an unlockable skill? Obviously (and this really, really should go without saying), he picked it up from his present self and (after a few botched attempts) eventually got the hang of it.
Why, in the 3DS version, is Shadow faced in Radical Highway instead of outside the Space Colony ARK - besides technical restrictions, that is? Because this way, Sega killed two birds with one stone. In Sonic Adventure 2, the final race between him and Sonic was right after Final Rush (or Final Chase), but if you remember, their Mirrored Confrontation Shot in Generations is lifted from the intro to SA2 instead. And where were Sonic and Shadow racing during the intro movie? Why, but in Radical Highway of course! Therefore, that level, besides being the one where you first play as Shadow in Adventure 2, suddenly makes perfect sense and becomes the ultimate Sonic vs Shadow stage. (Not to mention that this way, the intro movie to SA2 becomes a Hilarious in HindsightOffscreen Moment of Awesome.)
On that same note, one of the bosses from the 3DS version of the game is the Biolizard, also from Sonic Adventure 2. In the original game, the boss was fought by Shadow... But before he turned up, Sonic was getting ready to fight it — It took 10 years, but Sonic finally got to go one on one with the Prototype Ultimate Lifeform.
Why we can't see Dr. Eggman in the Death Egg Robot, even when he's kidnapped by the Time Eater? Why is such an effort to hide him made? Because it's his past, classic self, and it's not shown there to make the surprise in The Reveal. Also, when Eggman asked Sonic for help for the first time, Classic Eggman is genuinely scared.
Silver's appearance in the ending. Why does Silver remember Sonic & live in Crisis City? Simple, the events of Sonic 06 need to occur in order for Sonic to hit the Reset Button at the end of the game, so Silver's timeline still exists in order to prevent a Time Paradox. This also explains why Silver hasn't appeared in the main series since that game, as his timeline diverged with Sonic's death causing Iblis to be unleashed. With that in mind, the happy ending of Sonic 06 was actually a Bittersweet Ending from Silver's perspective, because he was still living in a post-apocalyptic wasteland — nowwithout Blaze — and if he travelled back to the point of Sonic Unleashed or Sonic Colors in the timeline, he'd be there afterSonic's death had already occured... But because of the Time Eater's actions, he was taken from Crisis City in the future & placed in the void alongside the rest of Sonic's friends, now from after the divergence of the timelines. So why doesn't he return to his native time after the Time Eater's defeat? For the same reason Marty McFly doesn't return to the 1985 where his dad's still being bullied by Biff; he's now at a point where the future has changed. In other words, it took five years, but Silver finally got a happy ending!
As for the Silver that appears in the handheld games after Sonic 06? He's from the post-Reset Button timeline, hence why their personalities & backstories don't match up.
Gets better. The Chaos Emeralds are capable of restoring memories and manipulating time and space. You battle Silver for the one in his possession during his rival battle, so of course him, and by extension, everyone else could now retain memories of Sonic 06.
On a similar note to the above theory, Sky Sanctuary Zone appeared to have been completely destroyed by the end of Sonic & Knuckles. So when Knuckles says it's "good to have (his) sanctuary back", he means it — he hasn't had it since 1994!
It also makes sense when you examine what is said about it. The Time Eater is a Humongous Mecha that was made from a living creature using both Doctors' genius — what was inside every mook you destroyed in the classic Sonic games? A little creature.
This also may provide a handy explanation for another thing. It explains why Eggman eventually tried to control things he really couldn't control: Because he saw himself succeed at taming one!
Although the Generations version of Speed Highway leaves out the "street level" portionnote the area that Knuckles explores of the original, there is a visual nod to it; both acts take place at dawn!
Why is Spagonia having a festival, and why are there flags of the other nations from Sonic Unleashed? Well, obviously, out-of-universe, it's to add some variety, because Rooftop Run was from the only other game to use both the Hedgehog Engine & the Modern Sonic-style levels; but in-universe? They're celebrating the restoration of the continents at the end of Unleashed.
Why does Silver ask if Sonic's really him, or "just a fake sent for Chaos Emeralds"? Well, the last time someone pulled that trick on him, all of time was nearly destroyed.
Modern Sonic's comment to Classic Sonic at the end may sound stupid due to some of his more lackluster titles... but if you see things from Sonic's point of view, you have to admit that his adventures are pretty kick-ass. While we're probably suffering through the games, Sonic is having the time of his life!
It's entirely possible that he's forgotten about the events of 2006. Even if he hasn't, note that he wasn't present for Silver's desert stage or the penultimate level, and the closest thing he had to truly unlikeable levels were the "Speed Up" portions, which as far as he's concerned went off without a hitch and certainly without plowing into walls. He also lacked the fandom's distaste for Elise.
The biggest downside to Heroes was being forced to play through similar stages four times. Sonic only did them once, and he was spared the more annoying members of the supporting cast while finally being in a position to trust and be trusted by Knuckles. And hey, he got to fight Metal Sonic again!
And being a Werehog? It's more fun on the other side of the screen.
The placement of Sonic Heroes. In the HD version, Seaside Hill is a Dreamcast-era stage, while in the 3DS version, Egg Emperor is a Modern-era boss. Which makes perfect sense, because Heroes had gameplay and level design similar to the Dreamcastgames it directly followed, while its runningboss battles seem to foreshadow Unleashed and Colors. (Though Sonic Advance 2 did it first.)
At the end of the game, Classic Sonic attempts to do a Homing Attack but fails; it is interesting in that the attempt basically looks like an Insta-Shield, a move that appeared out of nowhere in Sonic 3 (presumably after Sonic Generations in Classic Sonic's timeline) and has never been seen again since. Moreover, a proto-homing attack also appears in S3&K when you play as Hyper Sonic, which means that the Insta-Shield was actually Sonic practicing the Homing Attack, a move that he at first could only master in Hyper form.
You also forget the proto-Homing Attack from Sonic 3D Blast (only usable with a Golden Shield, and forced Sonic to drop to the ground) and the Jump Dash offered by the Fire Shield.
This is double Fridge Brilliance when you think about Sonic 4, where by this time, Sonic has mastered the Homing Attack and can Jump Dash without a Fire Shield.
All this enables one to theorize just where in the timeline Classic Sonic originates from: Sonic 2 or Sonic CD at the latest. The interesting implication is that if this theory is correct, Sky Sanctuary is as new to Classic Sonic as Planet Wisp was!
...You're forgetting the Sonic Advance games. Sonic could use the Insta-Shield in all 3 of them (albeit only with certain partners in Advance 3), though he also had the Homing Attack in Advance 2 and Advance 3. The Advance games' Homing Attack had trouble locking on to bosses, but worked just fine on mooks (and Sonic would preferentially execute a Homing Attack if the player held the directional input towards the enemy). As for where the Advance games fit in the timeline? Advance 1 probably takes place shortly after Adventure 2 (but could take place anytime between Sonic 3 & Knuckles and Advance 2), Advance 2 takes place some time between Adventure 2 and Heroes (Cream's introduction means that it can't be before Advance 1 or Adventure 2), and Advance 3 has to take place after Sonic Battle (which seems to take place after Shadow the Hedgehog). It's interesting to note that the Insta-Shield is gone from the Sonic Rush games, having been completely replaced by the Jump Dash (which only existed in the Advance games in a very clunky and risky fashion, forcing Sonic out of his Spin Attack to use; Rush's Jump Dash works just like the Adventure/Heroes/Generations version, with Sonic not uncurling until the end of the move).
Modern Sonic telling Classic Sonic that his future will be great. Sure, we had the debatable Dork Age of the 2000's, but considering that Sonic Colors and this very game have been very well-received, Modern Sonic is right in the long run.
A lot of people complain about how the majority of Modern Planet Wisp is in 2D, despite already having Classic already being 2D entirely. However, when you remember that this is the level representing Sonic Colors, which was mostly 2D with short bursts of 3D, this makes perfect sense. In fact, most of the 3D platforming in the Generations level was in the natural, untouched parts of the planet, which was never really explored in Colors.
Likewise, one of the most boost-friendly levels in the game is Rooftop Run, the level from Sonic Unleashed.
In the post credits ending, Classic Eggman asks Modern Eggman if they ever win against Sonic. Eggman says "define win." Egmman had defeated Sonic in a race in Sonic Riders, but because the treasure he was trying to get from Sonic was just a carpet, Eggman pretends that empty victory never happened.
During the final boss fight, the boss will sometimes slow time down, making everything really sluggish. The game's clock is also slowed down during this effect and runs at a much slower pace until the effects vanish.
Super Sonic's Nerfing actually makes a lot of sense considering how you get him. In most games, where Super Sonic is a Game Breaker, you obtain Sonic's Super Mode after going through the insanely challenging special stages, all of which are very hard to get to and also very hard to complete. The game rewards you for completing these extra challegnes by giving you an awesome Game Breaker. However, in Generations, you just get Super Sonic simply by completing the game normally. As such, the game doesn't give you much of a reward if you just went through the game without putting in any extra work.
The two oddest levels to appear in the game, Stardust Speedway's Bad Future and Crisis City, can have their appearances explained just by the power of the Time Eater. This troper suspects that the Time Eater isn't just limited to one single timeline, and thus can pull out the two levels through the alternate timelines that they come from (although as mentioned below, Stardust Speedway doesn't need this explaination because its appearance in Sonic 4: Episode II means it's canon).
The Death Egg appears in Sky Sanctuary Zone, as it did in Sonic & Knuckles. The boss battle that immediately follows takes place in the Death Egg, albeit the Sonic the Hedgehog 2 version.
Tails explains that he was basically in a living paralysis while trapped in statue form, and that it was horrifying. He was rescued first after a fairly short level, so the rest were probably in worse shape and hiding it.
Even better, the last one to be rescued? Charmy. As in, the six year old.
In Sonic 06, it is said that the events of the game never happened before the end of the game. And yet, in the Modern era, Crisis City still exists. There are two explanations: Time Eater forcibly brought it back to existence, or Crisis City still exists in the future.
Either that, or when Crisis City and the events of '06 were erased, it ended up in the White Void.
It's implied that the Time Eater can access alternate timelines, and possibly confirmed by Word of God, but I don't have a source on hand.
In Sonic Adventure 2, the Biolizard fell to its apparent death after its defeat by Super Sonic and Super Shadow, but, like many other characters ripped from the continuity of their time, is brought into the void of the White Space by the Time Eater. This implies that the Time Eater has resurrected the Biolizard. Meaning that for the Biolizard, it has been forced back to life in a familiar fight, suffers painful defeat by the hedgehog that originally intended to fight it first, and finally ends up dead again when continuity is restored. If Sonic and his friends are aware of the continuity displacement of the White Space, it can only be imagined what the Biolizard is aware of...
Likewise, with the appearance of Crisis City and Iblis' minions, it could be assumed that within the scope of that level, Iblis is also resurrected, and to the other half of that extent, Mephiles as well. Never mind being resurrected from the dead, but being resurrected into an existence for what has been erased from existence/should not exist in the first place. Try putting yourself into Iblis' level of awareness.
Sonic never beat Perfect Chaos in his rematch, at least not completely. In Sonic Adventure, it is mentioned that the positive energy from the Chaos Emerald that Sonic used in his Super form neutralized the negative energy Perfect Chaos used in its transformation, thus reverting Chaos back to its base form and dissipating its hatred. However, in the rematch, Sonic doesn't use his super form to beat Chaos, ergo, Chaos's hatred is not neutralized by the positive energy of the Emeralds, ergo, Chaos will continue to wreck shit in its fury.
Or, regular Sonic only managed to weaken Chaos for Super Sonic to finish off.
Or, it might be that Sonic had grown more powerful over time that he's able to take on Perfect Chaos without having to go Super. Besides, in Sonic Adventure, he can't perform a boost to run on water like he can in his Super Form. But, by the time Sonic Unleashed comes around, he is able to go fast enough to run and even turn on water. True, he possibly still was only able to weaken Perfect Chaos, but still!
We learn in this game that the Metal Sonic race from Sonic CD took place in the Bad Future. But, in order to get the good ending of Sonic CD, you need to get a Good Future in every zone, and if you miss one, you need to get all the time stones for the good ending, which means the future is always a good future, but you can't get them after the Metal Sonic race. So, this game has confirmed the bad ending of Sonic CD as the canon ending.
Then again, as mentioned above, the Time Eater could've just sampled from an alternate timeline where it was canon.
Okay, I know that Metallic Madness is evil beyond compare, but is it really impossible to get a Time Stone in that level?
Yes, it's like how in Sonic 1, the Special Stages are closed off during Scrap Brain, even when you get 50 rings.
Sonic the Hedgehog 4 Episode 2 has Eggman retrieving the broken-down Metal Sonic from the Bad Future, pretty much as it looks in Generations. Considering Sonic 4 is meant to be an interquel between the third game and Adventure, this theory was confirmed.