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.
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.
Best Level Ever: 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.
"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.
Moral Event Horizon: 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.
Narm: Black Doom's voice is so ridiculously raspy and exaggeratedly evil (think Claw), it is very hard to take him seriously.
To be honest, just about anytime anyone anywhere in this game attempts to be dramatic qualifies as this. There's a reason why this writing staff was completely fired just one or two games later.
Nightmare Fuel: Taking too long on the Last Story allows you to hear Sonic, Tails, Knuckles, Amy and Eggman slowly choking to death on nerve gas, still cheering you on with every last breath.
Porting Disaster: This game was built from the same engine as Heroes, and thus the PS2 release of this game suffers from all of the same problems the PS2 version of Heroes did.
Scrappy Mechanic: 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 Game Cube 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-> 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 Creepy 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.
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 hand of. However, the level terrain often repeats itself, and eventually having to search for things to complete the game quickly wears out its welcome.
That One Level: 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.
True Art Is Angsty: Possibly the reason the game was created, and a common reason for it to be enjoyed.
Unfortunate Implications: Although it's a pretty major stretching of the truth, a lot of the aforementioned negative Amazon reviews close to release included complaints about the "white soldiers" defending against the "black aliens" (worth noting is that technically the Black Arms aren't actually black, but brown or grey). It's some pretty awful nit-picking, considering how many games involve dark-coloured villains. They seem to be missing how the hero Shadow is also black.
Before the game came out, VG Cats did a comic joking about how Shadow, a black hedgehog, would have a gun, and that the rings would be replaced by watermelons.
At the end of the Hero mission of the first level, Sonic and Shadow pose while Shadow says, "Disgusting black creatures. Get out of my sight!" It's... difficult to un-hear or forget.
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.