- Broken Base: Pokémon Shuffle shattered the fanbase when it was revealed to be a free-to-play game. Some fans think it's free-to-play model will be perfectly tolerable, while others think it will pave the way for more abusive microtransactions in the future.
- Difficulty Spike:
- Battle Trozei! starts using Legendary Pokémon as bosses in world 3.
- The original game gets more difficult on the 4th Phobos General, Aquarella.
- Fridge Brilliance / Genius Bonus: The Phobos Battalion's symbol is a Lunatone. Phobos is one of the moons of Mars.
- That One Attack: In the sequel, any Pokemon that can change what Pokemon are in your box. This potentially disrupts any Trozeis you have set up, and usually adds copies of that Pokemon into the box, which take up space unless you manage to get a Ditto.
- Shaymin Sky Forme will give you a game over with just one attack, no matter how much life you have.
- That One Boss: As noted above, Shaymin Sky Forme. You'd best be fast!
- Landorus. The fact that you have to bring in Tornadus and Thunderus as supports just to fight it is bad enough, but in order to unlock another zone, you have to flawlessly catch it. Unless you bring in a third support that is Super Effective against Ground-Types, good luck.
- That One Level: In the sequel, any level where the stage Pokemon in your box are too similar in color.
YMMV / Pokémon Trozei!