* AnnoyingVideoGameHelper: Tails feels the need to remind you to save your game ''constantly''. He tells you to save before or after pretty much every major plot development, to point of being a RunningGag. It's clearly done intentionally too, since there's multiple points where you can have Sonic make him shut up.
* AngstWhatAngst: Subverted. At first it seems that none of Sonic's pals seem too annoyed about him pretty much just abandoning them all at the drop of a hat to run off on adventures once Eggman is beaten. But through some dialogue options later, it becomes pretty clear that there's plenty of resentment bubbling just underneath the surface. Knuckles finally flat out says it after the party rescues him while Tails and Amy are too polite to say anything and try (poorly) to pass off the question.
-->'''Knuckles''': You're not [[TheLeader the boss]] anymore Sonic.
-->'''Sonic''': (Disbelieving) Do the rest of you think this?
-->'''Tails''': ...... [[TearJerker You were gone a long time Sonic]]...
* AwesomeMusic: [[SubvertedTrope Not this time sadly]], it's one of the most constantly loathed aspects about the game by the fandom, but a select few do the [[AwesomeMusic/SonicTheHedgehog series record justice]].
** The [[https://www.youtube.com/watch?v=ARy1oZ1wfhs opening theme]] (of which a variation plays when getting ambushed in battles) is actually pretty great, as are the battle themes.
** [[https://www.youtube.com/watch?v=mq6Vl_UJhkI The]] FinalBoss music is superb and good to listen to [[LongSongShortScene if the]] [[AntiClimaxBoss battle wasn't so short]].
** The [[https://www.youtube.com/watch?v=3FUPdG8vEuc boss battle]] sounds clean and fine.
** [[https://www.youtube.com/watch?v=zzGYztkYB70 Mini Boss Ix]] is quite catchy.
** [[https://www.youtube.com/watch?v=N3dQRp74A3Q Mystic Ruins]] is not bad at all.
* DemonicSpiders: Nearly every enemy during the second half of the game if you don't grind on the first playthrough. Their ability to take and give damage rises spectacularly.
* DisappointingLastLevel: The first half of the game starts off rather nice, but then about 25% of it gets rather annoying. You're still learning everything, the game chucks a bunch of high defense or high-dodge enemies you can't kill by melee attacking at you, Robotnik only helps one team at once, etc. But once you reach the Twilight Cage, the game gets much ''much'' better.
* EnjoyTheStorySkipTheGame: General consensus is that the game has some of the best dialogue and story elements of a ''Sonic'' title in years due to Bioware's characterization.
* FranchiseOriginalSin: This could be considered the point where Bioware's viability started to ebb. Also a daily double because it riled comic writer Ken Penders to the point where it actually HURT himself, Sega, and Archie, possibly more than ''[[VideoGame/SonicTheHedgehog2006 Sonic '06]]'' did.
** Cream is by far the best healer in the game, especially if you give her the Chao that allows all of her special techniques to work without fail. Level her up enough, and Cream's POW restoring move recovers more for the entire party than it costs her to cast it, allowing you to spam everyone else's strongest techniques without fear of running out of POW.
** Knuckles + [[spoiler:Shade]] makes for a ridiculously strong team. A few perfectly executed Echidna Rushes is usually enough to take out almost anything.
** Shadow has an attack that has a 50% chance of completely [=KOing=] an enemy. Equip him with a Unique chao that can give you a chance for an instant KO, and use his bonus level up points on his luck stat, and you have a force to be reckoned with.
** The "Immortal Big" set up, especially against bosses. There is a rare Chao that forces enemies to attack its user. Combine with Taunt and Feel No Pain, and watch that boss be forced to attack something it can barely hit, and only scratches even when they do connect. Combine with Cream's POW restoring abilities, and most bosses are reduced to a joke.
* HilariousInHindsight: One of Tails's most often used and helpful healing skills? The [[LetsPlay/SonicTheHedgehog2006 Medibot]].
* MagnificentBastard: [[spoiler: Dr. Eggman got a serious upgrade from his usual self into this. He admits he didn't know if Sonic and the others would come back but ''hoped'' they would so he could show off.]]
** [=QUALITY BIOWARE SOUNDTRACK=]
** "[[https://www.youtube.com/watch?v=MLAzVPaREIE They've got a new Sonic character! I must draw porn of it!]]"
* RescuedFromTheScrappyHeap: One of the reasons the game gets such praise for its writing is taking the worst aspects of some characters and making them much more palatable. Big's stupidity is made into ''funny'' stupidity rather than plain old dumbness. Also Amy Rose, who was dialed back from StalkerWithACrush to just a ClingyJealousGirl. Cream is also much less annoying, preferring to hang back and let the other characters do the heavy lifting.
* ScrappyMechanic: How you execute the POW moves, which require EBA-style rhythm minigames. Sometimes it's OK, sometimes it's bad and sometimes it's ''horribly unfair''. Doesn't help on how nice some of the POW moves' effects can be - because if you mess up even a ''little'' bit, oops, you just wasted a turn and a nice ton of PP! It certainly doesn't help that this is the ONLY way you can counter enemy's attacks and execute your own. And what if you don't have a stylus or a very good touch screen?
** Arguably, the defense of some of the enemies. It can be ridiculously hard to hit them at the best of times, but then most of them will go on defense, making it either impossible to hit them or you can only knock off one point of damage at a time.
** Any time an enemy flashes "Evasive" Be prepared to spend an entire round watching your character fall flat on their faces turn after turn after turn...
* SoOkayItsAverage: The game has a good story, great characterization, and creative gameplay mechanics, but is brought down by a lack of content, unbalanced mechanics, and an awful soundtrack. It's generally considered to be at least enjoyable, but nothing excellent.
* ThatOneBoss: Better hope you grinded to the point of invincibility before the penultimate fight with Ix. If you're not leveled up enough, don't have a good enough character combination, or if the equally annoying battle with Scylla and Charybdis drained your supplies, you're gonna get your ass kicked ''hard''.
* TheyCopiedItSoItSucks: Penders played this card HARD on Bioware and Archie for using expies of several Archie Sonic characters, destroying his reputation and putting the planned sequel in prolonged DevelopmentHell (which it was already in for the middling reception it got in the marketplace, which, along with the initial tepid reaction to ''Sonic Unleashed'', did not help Sega or Sonic's DorkAge and led to a turnover at Sonic Team.)
* TheyWastedAPerfectlyGoodPlot: While the game turned out okay, a lot of fans feel that it could have been ''awesome'' if Bioware hadn't rushed it to focus on ''Dragon Age''.
* WhatAnIdiot: [[spoiler:Shade]] defects from Ix's service after learning he wants to conquer Earth. Except the Nocturnus were conquerers before they were sealed in the Twilight Cage, and they conquered everyone ''within'' the Cage, so it's a wonder how the aspiration to keep conquering would be so much a shock.