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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.
The "Eggman" Remix. He's listening to it in-game and there's a full version of it on the soundtrack.
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 Gary Stu who should have died after his debut and just does not fit with the whimsical nature of the series.
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.
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.
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.
Deader Than Disco: Believe it or not, there were a lot more defenders of this game when it was first released. Perhaps due to the increasing backlash towards Darker and Edgier Sonic past Sonic '06, the fandom's revulsion towards the game slowly built up to the point that it's nearly as hated as '06.
Fan Favorite: Shadow, to the other half of the Sonic fan base.
"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.
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.
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 no "extra" enemies/stuff to find if you miss a few, and the only way to backtrack is to move right past the goal right to the beginning. And all of these problems wouldn't be too bad, but the linear stage design just makes them unbearable.
So Okay, It's Average: The gameplay pretty much averages out to being... Adequate. The core gameplay is excellent, the guns actually work with good auto-aim and decent damage, and the controls (though slippery) can be easy to get the hang of. However, the level terrain often repeats itself, and eventually having to search for things to complete the game quickly wears out its welcome.
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.
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." Also, the Good/Neutral/Evil routes barely have an impact on the story, despite massive potential over who would see Shadow as an ally or enemy.
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.