* 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]]...
* 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.
* GameBreaker: Cream, 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. Hello, sweet, sweet free healing and PP recovery!
** Knuckles + [[spoiler:Shade]] makes for a ridiculously strong team. A few perfectly executed Echidna Rushes is usually enough to take out almost anything.
*** [[spoiler:Shade]] and Sonic also work pretty well too.
** 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.
** Cream + Omega. Both side quest characters, Cream broken, Omega beyond powerful.
** The "Immortal Big" set up, especially against bosses. There is a rare chao that forces enemies to attack its user. Combine with Taunt, then Feel No Pain and watch that boss be forced to attack something it can barely hit let alone hurt. For additional lulz, add Cream and let her fuel the big lug's tanking engine.
* 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.]]
* MemeticMutation: [=QUALITY BIOWARE SOUNDTRACK=]
* ObviousBeta[=/=]TheyJustDidntCare: A lot of people feel this way because Bioware evidently finished development as fast as possible because they finished their contract(s) to Sega. The music got the worst budget cuts: supposedly there was ONE GUY with a MIDI keyboard to make the few original tracks, and padded out whatever he didn't have time for with MIDI versions of music from older ''Sonic'' games.
* RescuedFromTheScrappyHeap: Big, done by taking his stupidity and making it ''funny'' stupidity rather than plain ol' retarded stupidity. Also Amy Rose, who was dialed back from StalkerWithACrush to just a ClingyJealousGirl. Cream is also much less annoying.
* 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...
* StopHelpingMe: 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.
* ThatOneBoss: Better hope you grinded to the point of invincibility before the penultimate fight with Ix. If your 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 your gonna get your ass kicked ''hard''.
* 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: A certain character 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.