Starter Pokémon is based off the player's Trainer ID number. If the last number is 1-3 the player starts with a Grass type, 4-6 is Fire type, 7-9 is Water type, 0 is the player's choice.
Species/Dupes Clause: Adjusting the first encounter rule to ban duplicate captures.
Not officially enforcing the rules until the player has Poké Balls and can catch Pokémon. For example, the Poochyena/Zigzagoon that the player has to save Professor Birch from in Ruby/Sapphire/Emerald is not counted as the first encounter on the route, and not counting any other encounters as such until they can catch.
Likewise, in the games where the rival battle is immediately after getting the starter Pokémon, the "any that faint must be released" rule is not enforced at that time.
Use the same amount of Pokémon as the opponent during a Gym battle or rival battle.
Going to options and making the battle style "set", leaving the player unable to switch out.
After the first wild Pokémon was caught, the starter Pokémon must be released.
Banning the use of Potions and healing items, relying only on Pokémon Centers for healing.
Banning the use of Pokémon Centers, relying only on Potions and healing items for healing.
Limiting Pokémon Center visits to a certain number per town.
Banning the use of held items.
Limiting the number of Poké Balls to purchase per Poké Mart.
Banning the use of Master Balls.
Rather than releasing the Pokémon, it can be permanently boxed, migrated, or transferred with Poké Transfer should it happen to faint.
The player may not evolve captured Pokémon, but evolved Pokémon may be caught.
Turning the difficulty on to Challenge Mode if playing Black 2 or White 2, which increases the levels of opposing Trainers.
No catching/using legendary Pokémon.
As a mercy rule, allowing 1-3 "second chances" or revives of fallen team members.
As another mercy rule, if the player runs into a Shiny Pokémon on the incredibly rare chance, the player may still catch it, regardless of whether or not it is the first encounter in the area. It also does not need to be released if it faints.
As another mercy rule, each gym badge acts as a checkpoint. If the player gets a game over, they can start from when they got their previous gym badge.
If the player has no Pokémon that can use a certain field move that is required to continue through any given point of the game, they may catch another Pokémon that can learn said field move.
However, it cannot be used in battle for any reason, and must be released, permanently boxed, or migrated as soon as the player gets another Pokémon that can use said field move.
Modifying the "first encounter only" rule for the Safari Zone, sometimes allowing one encounter for each area, or until they catch one Pokémon in the entire area, and vice versa.
Banning the use of Poké Marts.
Disallow fleeing.
Setting a level limit based on the next Gym Leader's/Champion's highest leveled Pokémon. Any team members that surpass that limit before taking on the Gym Leader or Elite Four must be released.