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.
It can be argued that music describes what goes on in a character's head in ways that dialogue can't. The Chosen One does a great job at proving this point by explaining how Shadow regrets the doom that he brought to the world, but in the end, he is the last hope for humanity.
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. 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.
"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.
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.
Scrappy Level: Lost Impact takes far, far longer than any other level in the game, and is an even more blatant scavenger hunt than any other level.
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.
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 Doom is annoying to complete the hero mission (Maria's) for, since getting all the health packs requires a lot of time and backtracking, although it's not so much difficult as it is tedious (instead of doing that, you can just use the Heal Cannon to heal them).
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 most of the Black Arms aren't actually black, but brown or grey). 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.
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.