- Broken Base: The story. Some consider it to be well-written mainly because of the character interactions and Emerl's story arc while some find it to be annoying due to the flanderization of some characters, the long dialogue in the cutscenes, and the plot where characters fight each other to train Emerl.
- Character Tiers: Two tiers in particular are such outliers that it basically becomes:
1. Emerl at the end of the gamenote
2. A couple of tiers of everyone else, depending on their healing skill.
3. Emerl at the beginning of the game.
- Enjoy the Story, Skip the Game: The gameplay is decent but considered to be too repetitive and nothing spectacular. The game's main draw arguably comes from Emerl and his character arc throughout the game.
- Game Breaker: So many it has its own page.
- Iron Woobie: Emerl.
- Moral Event Horizon: Eggman making Emerl go berserk at the end of the game, after Emerl was nice to him and thanked him for waking him up.
- Narm: "...and shall become Gizoid, the conqueror of all..." is hard to take seriously, due to having an Inherently Funny Word in the middle of it.
- Nightmare Fuel: Emerl's stated purpose when he finally obtains all the Emeralds.
- Paranoia Fuel: When in distress, or receiving an upgrade, Emerl sometimes looks directly at the player, gains a third eye that looks realistic and stares out of the screen, is shaded ominously, and speaks in a strange, stilted voice. Tails Doll's got nothing on this.
- Player Punch: After spending a huge amount of time learning about Emerl and training him to be an amazing fighter, Sonic has to destroy him.
- Self-Imposed Challenge: If you're feeling lucky or are otherwise just confident in your skill, try to get through the whole game using nothing but Emerl's initial moveset. You'll probably be fine.
- Scrappy Mechanic: The ridiculous number of storyline fights that are immediately followed by, essentially, the same fight but with twice the KOs. This may have been an attempt to increase the number of Skill Points available, but if so, there were better options.
- That One Attack: For many it's Gamma's Recovery Mode. He does spell it out for you, however, and after minimal practice it should be easy to be able to guard it. The high power makes it give you a LOT of meter. Now, when a Guard Robo or Phi has this, you're in real trouble, because they don't go announcing it.
- Eggman has a similar one, except it comes out immediately when he's K.O.ed; the upside is however is that it doesn't have a big radius around himself and he'll suffer from a bit of knockback at least give you some distance when it happens.
- That One Boss:
- Eggman can be one given his missile spam and tendency to explode when knocked out.
- The fight between Rouge and Team Sonic at the end of the third chapter. Being forced to fight three against one is just torturous unless you stay in the air and pick them off slowly, or if they didn't set their auto-block to your Ground Power move.
- The Guard Robots as Knuckles. At first it's not bad, with just one. Then you fight two. Then three. No breaks in between. If you're not good with Knuckles, this is a nightmare.
- Any Phis copying Gamma, especially late-game. If you have any allies you can't afford to have give free K.O.s to them, then for sure you'll be having trouble trying to keep them alive since they'll never move away from his suicidal explosion. Your best hope is usually a CPU-controlled Emerl with the highest defense setting possible if you managed to unlock it (Shadow Style + Shadow Strength Support).
- Ditto with the Guard robots. Since they don't talk, it's difficult to dodge Gamma's "Recovery" Mode with no audible cue.
- The fight with Rouge where Emerl has to get 10 KOs without using any special moves. It can be somewhat mitigated with a good setup however. If you have the Character Combos from the final chapter, the game will not count these certain ones as special moves.
- The Sonic and Shadow fight before the final chapter. Sonic and Shadow, who have huge handicaps to make them competent fighters, against an Emerl player who's still trying to find the perfect moveset to stick with. Not even the unlockable combo attacks will guarantee a kill.
- The first fight against Knuckles as Emerl can be this. At this point of the game, you'll have very few skill points for Emerl to use many skill cards for attacks. Many of Emerl's attacks will be slow and weak. And depending on how you arranged your skill cards, he won't be able to jump that high, or his movement could be incredibly slow. This definitely makes things a challenge when fighting the powerful and fairly quick Knuckles.