Digital Circuit. And if you like that, you'll like Mad Matrix. Not only is the Cyberspace concept a very unique one among Sonic levels, but the sections where you race along internet circuits are really fun, and the platforming is quite well-done in the level. Technically there are puzzles, but they require something less than the brainpower of a slug to solve.
Lethal Highway. Of all the levels in the game, it's the closest in terms of design to the well-received Sonic Adventure 2, meaning that you can just skate along the highway at full speed, and near the end, it homages Speed Highway. It also has motorbikes.
The Dark mission in Air Fleet - chasing and shooting down the president's escape pod - is a wonderful mix of fast-paced Sonic gameplay combined with third-person shooting. It's one of three missions with that mechanic, one of the other two being Lethal Highway above.
Circus Park is a bright colourful amusement park with lots of great level gimmicks, Eggman being really exciteable about it due to him creating it, and good uses of the gunplay, such as in shooting gallery sections.
GUN Fortress. Unusually melancholy music, wide open spaces, lots of space to run around, a sense of progression that many levels in this game don't have, and a Dark mission where you can cause massive carnage.
Sky Troops, which has a great sense of speed and platforming, set high up in the sky with great music and pretty good missions. It was popular enough to be included in fan mods of Sonic Generations.
Base Breaker: To elaborate, the base was already pretty broken over if Shadow's return in Heroes was a good thing or not. This game did nothing but add fuel to that fire. In fact, this game cemented Shadow as the most divisive character in the series bar none. To this day, fans are split on whether he is still a good character who's just been the victim of overexposure and bad writing, or a glorified Marty Stu who should have died after his debut and just does not fit with the whimsical nature of the series.
Big Lipped Alligator Moment: In the ending, Eggman demands for the Chaos Emeralds while sneaking away with Knuckles chasing after him as Sonic and the others start laughing.
Because of how many combinations of level sequences there are (326!), this happens sooner or later.
Breather Boss: The Egg Breaker in Iron Jungle (and Iron Jungle only, Mad Matrix and Cryptic Castle have harder fights) is ridiculously easy if you go behind the start and spam the turret. You can beat Eggman in 7 seconds this way.
The Doom's boss fight against Heavy Dog. It's fairly annoying, but not difficult, especially considering how horrendous The Doom can get in all three of it's missions.
The Egg Dealer, which appears as the final boss of four of the ten endings, is also not particularly difficult or annoying compared to Black Doom or Sonic and Diablon who both fall right into Goddamned Boss territory.
Breather Level: Any level where you just have to get to the end, especially if you were doing Hero or Dark missions before. Getting to the end is easier than finding stuff. However, The Ark's Normal mission stands out - all you do is just fly on a Black Arms bat thing for the entire level, only you were required to do the Dark missions of either Central City or The Doom to get here, both of which are That One Level and detailed on this page.
Complete Monster: BlackDoom is the leader of the Black Arms and a completely humorlessEvilutionary Biologist. Having visited the Earth for thousands of years, he made contact with Gerald Robotnik 50 years prior to the series, agreeing to a deal where a creation using Black Doom’s cells, the future Shadow the Hedgehog, would deliver the Chaos Emeralds so that the Black Arms can use Chaos Control to arrive on Earth and bring prosperity to humanity. Gerald realized once Doom left that he was lied to, as Black Doom intended to enslave the human race and use them as a food source. During the events of the game, he preaches about the evils of humanity and how they don’t deserve to be free, claiming they would be better served as a food source for the Black Arms, all while showing he has no regrets killing his own men or throwing away his “son” when everything is finished. During the game, he sends his army to kill millions, manipulated Shadow by forcing him to relive Maria’s death, destroys an entire city—and most of his army—with the Eclipse Cannon, and spreads a gas that paralyzes Sonic and friends to make it easier for his offspring to eat them. Hypocritical, ruthless and uncaring to even his own, Black Doom is among the worst the world of Sonic the Hedgehog has to offer.
Creator's Pet: What half the Sonic fandom sees Shadow as. Considering it has actually been confirmed that Shadow (and Sonic) are Takashi Iizuka's favorite characters, and Iizuka being Shadow's creator, it not hard to see why.
"Find the Computer Room!", which both the fanbase and SEGA launched on top of to create the sneakiest injoke of Summer of Sonic '09 - in particular, putting up confusing signs to the computer room. Of course, it's also in the placeholder for Sonic City, and even became the name of a website.
"Looks like these black creatures really mean business!" and various other lines in game to that effect are popular to bring up, making fun of the fact that everyone constantly seems to want to mention what color the aliens are in a way that makes it very easy to pretend the characters are all psychotic racists.
Shadow puts his current total of five Chaos Emeralds into the Eclipse Cannon and uses it to completely destroy a capital city. But then, this trope is averted thanks to No Endor Holocaust.
On a different path, Shadow deliberately tries to kill the fleeing president, who is previously shown to be almost comically upstanding (and to have a great deal of respect for both Shadow and Sonic). Shadow fails to accomplish this as well.
His final chance to cross it for certain paths can count as a success. In three of the endings, he decides to kill everyone's favorite eggheaded scientist.
The weapons actually work better than you probably expect, but the vehicles are not so polished — especially the motorcycle that shows up in the intro movie. The walkers work pretty well, though.
The effectiveness of the weapons depends on what version you're playing. Works pretty well on the Gamecube version but is utterly useless on the PS2 version. Also, the targeting system seems to have issues when it comes to short-ranged weapons, yet works really well once you start getting medium to long-ranged weapons.
Additionally, no matter which path you take in a level, all the enemies will attack you, which forces you to kill them and have your assist character chew you out for it. Notable in Cryptic Castle, where Eggman is the Dark assist character, but whether you choose to go with him or Amy, both of them will chew you out when you destroy Eggman's robots. This is especially bad when you need to defeat enemies to proceed, even if doing so will raise the gauge opposite of the mission you're going for, lowering your score.
The "hunting" missions of every kind are terribly designed, which really hurt as they comprise about 60% of the whole game. You have no radar, and there are rarely "extra" enemies/stuff to find if you miss a few, and the only way to backtrack is to keep moving forward until you find another checkpoint. And all of these problems wouldn't be too bad, but the linear stage design just makes them unbearable. Team Chaotix had something like this in Sonic Heroes, only there you were only required to find half the things most of the time, rather than all of them, and there were more colours in that game so things stood out more.
So Okay, It's Average: The gameplay pretty much averages out to being... adequate. The core gameplay works out well despite somewhat slippery controls, and the guns actually work with good auto-aim and decent damage. However, the game suffers from levels with repetitive design, along with missions that make the game even more repetitive.
Cosmic Fall is a MAJOR pain in the ass because of the numerous tricky jumps over rotating platforms, and you'll have to fight with the awkward camera throughout the entire level; good luck beating this level on hard mode! The main saving graces are that both of its missions are to get to the end of the level (one is just further away), and parts of the mission are very fast.
The Doom is easy to get lost in even with the use of the maps, which are as confusing as they are helpful, and the carrying of the Heal Units slows Shadow right down. Its (slightly) saving graces are that if you see a Heal Unit, you know a scientist is close-by, and how easy it is to use Chaos Blast over and over again thanks to the amount of destructible scenery.
Even with The Doom slowing things down whichever way you play it, Lost Impact is the hardest, most tedious level in the game. It's slower due to the slow-moving GUN Lifts, with more Artificial Chaos to hunt - not to mention they are a powerful enemy. And on top of everything else, they are just about the only enemy that gives Hero points, so you won't even charge Chaos Control to speed your way in the Neutral mission.
Central City. Take the bland visuals of Westopolis, add the maze like elements of The Doom and Lost Impact with the same issue of repetitive confusing visuals, no goal ring (so no Neutral mission to speed through), and an 8 minute time limit.
Black Comet. Visually bland, repetitive level design, ridiculous length, and lots of liquid that acts as bottomless pits. It gets worse though - several sections require you to use the air saucers to manouver across masses of liquid, only aliens AND military soldiers alike are shooting the hell out of you, and if the saucer runs out of health, down you go.
They Just Didn't Care: Simply put, the game is not programmed to constantly recognize your current morality. Characters who should be on Shadow's side will still attack him, and there are points where Shadow is required to attack his supposed allies to progress. The cutscenes can also play out ignoring Shadow's actions, like Black Doom taking way too long to figure out that Shadow isn't working with him.
In Cryptic Castle, the Dark mission requires you to side with Eggman. However, because the Black Arms and the Eggman robots are both in this level, Eggman's robots contribute to the Dark points gauge (and thus, your Dark mission ranking), even though Eggman is scolding you for attacking them. In other words, attacking your own ally's mechs is the way to get points for that mission.
They Wasted a Perfectly Good Plot: The entire premise of Shadow deciding whether to be a hero or villain was simplified down to: "Maybe this guy knows about my past... no maybe this other guy." There's no involvement of actual character morals whatsoever, and the Random Events Plot nature of whatever route you take blocks out any Character Development we might see from Shadow. Also, the Good/Neutral/Evil routes barely have an impact on the story, despite potential for compelling storytelling drama over whoever sees Shadow as an enemy or an ally. There isn't even an ending where Shadow sides with Eggman!
In particular, Shadow's implied Robotic Reveal towards the end of Heroes would have made things even more interesting... But it's only even really mentioned in the last two of the neutral-route levels, and thus the two endings where Shadow accepts this as fact are two of the absolute least canon, even when taking the game's story before the Omega Ending as Broad Strokes. Instead, we just have to accept that Shadow had an Unexplained Recovery after Adventure 2. At least they do cover that Shadow was rescued by Eggman as he fell, so at least it isn't left hanging, but only if you wait 9 minutes into the final boss, as it's never in any actual cutscenes.
True Art Is Angsty: Possibly the reason the game was created, and a common reason for it to be enjoyed.
Wangst: This is the game that inadvertently set Shadow's characterization among the fanbase as this. Ironically, it's also the one where he actually gets over it.
We're Still Relevant, Dammit: Some see the game's Darker and Edgier turn as Sonic Team doing this. While the game did sell relatively well, the backlash and eventual reception to Sonic '06 along with issues concerning other aspects foiled their attempt to play this trope straight, leading to Yuji Naka backing out of Sega, Dimps being assigned onto the series alongside Sonic Team, and the Broken Base problem becoming worse.
What an Idiot: Eggman's Egg Dealer mech is a slot-machined mecha that has a power that can help Shadow out. Why would Eggman purposely add a device that he personally built that can help an enemy of his out?!