Permadeath: If a Pokemon faints, it is considered dead and can no longer be used. It must be either released or banished to a “Death Box” in the PC.
Mandatory Nicknames: All obtained Pokemon must be given a nickname so to grant them individuality.
Limited Items in Battle: During trainer battles, I am limited to the same items that the opposing trainer has. For example, if Lorelai has two Super Potions, then I can use two Super Potions in that battle and nothing else. During wild encounters, I can use as many items as I want.
Set Mode: The battle mode must be “Set”, not “Switch”. This removes the option to switch Pokemon after defeating an opposing trainer’s Pokemon.
No Over-Leveling: I can not intentionally train my Pokemon to be a higher level than the next major trainer’s highest level. This is a soft rule; a level or two may be forgiven if I mistake how much experience a Pokemon will gain or what the next trainer’s highest level is.
Gift Pokemon: Pokemon given to the player as a gift (not obtained by catching) can be used and do not count as an area’s encounter. This includes Pokemon given as an egg.
Static Encounters: Wild Pokemon whose appearance is scripted and can only be caught once (ex. Snorlax, Sudowoodo, Kecleon, most legendaries) are allowed to be caught and used. They do not count as an area’s encounter.
Legendaries & Mythicals: Mandatory legendary encounters must be battled, not run from or Master Ball’d. Captured legendary or mythical Pokemon may be used, so long as they are not banned to Ubers in that generation.
Duplicates Clause: If the first encounter in an area is a Pokemon I’ve already obtained (or in the same evolutionary family), I must reroll the encounter, regardless of whether or not that Pokemon has died.
Shiny Clause: If a (non-scripted) shiny Pokemon is encountered, I am allowed to catch and use it, even if it is not the first encounter in an area. This clause can not be exploited to obtain an extra Pokemon by intentionally shiny hunting.
Favorites Clause: If there’s a Pokemon I particularly want to use and either it appears in only one area or I have reached the final area where it can be caught, I am permitted to reroll that area’s encounter until I find that Pokemon. I am still only allowed one chance to catch the Pokemon. This clause can not be exploited to obtain Pokemon that are banned to Ubers in that gen (with the exception of Garchomp because it’s one of my all-time favorites).
Game Over: If all of my Pokemon are dead, both in the party and in the box, and I don’t have any more than can be used, the game is lost and I have to start over from the beginning.