If you are aligned with evil: your pokemon have lower HP (up to half), their attack and special attack stats go up but their critical hit chance and evasiveness go down, and wild pokemon are harder to catch.
If you are aligned with good: evasiveness and critical hit chance go up, wild pokemon are easier to catch.
You can sell pokemon on the black market and buy pokeballs that can catch any pokemon, even ones belonging to other trainers. You can rescue pokemon from poachers and persuade pokemon from evil trainers to join you.
