Because of many changes from the original game, there is much less planning and building to be done on a Touhoumon.
- TM06 Toxic (Poison type attack that can severely poison), TM 32 Double Team (evade up) and TM10 Bride Training (obtainable by Pick Up, and shops in unofficial patches), a 5 PP move that recovers half HP, can be learned by almost all Touhoumon.
- TM45 Morning Sun is now a 80 base power Grass Type special attack, not a healing move. It has a 10% chance to lower the opponent's special defence. It can be bought at Celadon for 3000 yen.
- HM 07 Waterfall has a chance to flinch the opponent.
- Judgement is the only one hit knock out move in the game, and is learned by Shikieiki.
- Seal Needle paralyzes, not poisons.
- Mud Sport does damage as well as weakening electric attacks.
- Hidden Power is not available.
- Coerce reduces the opponents PP from the last move it used.
- All Move Tutors are disabled on version 1.5x, except two. A girl on the second floor of the house (with a door) on the top left corner of Saffron City teaches Learning if you give her a Poke Doll bought from Celadon City Department Store and a man on the bridge south of the seventh island teaches Mind's Eye. These tutors are the only way in which some Touhoumon can learn these two moves.
- The Hyper Beams in this game are LUNATIC (Normal), Blast Burn (Fire), Hydro Cannon (Water), Sheer Cold (Ice) and Hisou Sword (Ground). Frenzy Plant is now HouraiPetals, which is a grass-type Overheat (equivalent to Leaf Storm from the 4th generation of Pokemon).
- Memento is a 220 base power Dark type move that KOs the user.
- The only Bug-types are Yamame (Bug/Ground) and Wriggle.
- The only Dragon-types are Iku (Dragon/Electric) Final and EX Meiling (Dragon/Fighting) and Kasen (Ground/Dragon).
- General Touhoumon balance is better than in the original Pokemon games. There's generally only about 10-60 total base stat difference between various Touhoumon. The only real exceptions are the 'legendaries' and novelty Touhoumon.
...as well as some aspects from the main Touhou games:
- Stage 6/Extra Stage bosses are not necessarily the strongest Touhoumon. Cirno, for example, is among the strongest Ice or Water types, and Shizuha is among the strongest Grass types.
- Many Touhoumon have signature moves drawn from their profiles, such as Yuyuko's Resurrection Butterfly and Marisa's Master Spark.