I did a Nuzlocke for ORAS with some people, and I had a much nicer time with that game compared to the original. I typed out our rules for a friend's blog, so I can easily dig them back up.
- In Memoriam: Any pokémon that faints will be considered dead. The use of Revives is strictly forbidden, as is raising mons from the dead in a Pokécentre. Should an NPC accidentally heal my party, we have to adhere to the honour system and still consider it to be dead.
- Gravekeeper: "Dead" pokémon will be deposited in the last PC box, which shall be our graveyard. This method will allow me to keep a neater log of our fallen comrades.
- Game Over: The Nuzlocke challenge will be officially over when we are completely wiped out and have no more Pokémon. At that point, well have to decide whether or not we have to start an entirely new save, or to continue playing Pokémon in the vanilla way using a boxed Pokémon and a deep sense of shame.
- Patriarchy Protest: We shall only catch female or genderless Pokémon. If we get a male Pokemon through trading, he should get boxed. If your starter Pokémon is a male, you should get rid of it once you have a second Pokémon that is at least level 5. We'll have strong independent women who wont need no man. *snaps fingers and bobs head* The reason for this rule is to be pickier with who we can catch, adding another layer of challenge.
- Highlander:We will only have one Pokémon per species. First one we catch of a species will be the one we stick with. This rule is to prevent catching the same few critters over and over again to avoid having to level or comparing stats.
- Pikachu is probably called Pizza in the UK: Any Pokémon we'll will catch will get a nickname. I want to see if this little bit of personalisation will make deads hit harder than they already will.
- Dittos Can Be Classy Too: We shall not use a Ditto for breeding Pokémon. Similarly, we can only breed Pokémon when the purpose is to donate an egg to someone else, or to get a pre-evolution form. Breeding for stats or natures is explicitly forbidden.
- Changing the guard: After each Gym, we'll box our highest level Pokémon and let her retire. This is to prevent powering through with only one or two heavy hitters. Retired pokémon can still be used for breeding.
- Is bliss supposedly: While weve technically already played this game before, in the form of the original, we will still play this version as blind as possible. This means we will not look anything up. This means no checking which Pokémon are available and where they are, no looking up Gym Leaders, no looking up levels of when Pokémon evolve,... nothing. The only thing we'll going on is what we know and what we can figure out through the game itself.
Some of the rules were silly, but I think arbitrary challenges is what Nuzlocke runs are all about. I definitely had fun, and had to think more about the usual flow of Pokémon games. Especially the retirement rule made things significantly harder, since the trainer levels raised, while yours dropped routinely. It did help us spread our levels out, and we did use the EXP share stuff.
Most of the run itself went great, with only 4 mons in my graveyard, but the Elite 4 was a massacre. The only mon that survived to see me become a poké champion was Guttertrash the Ludiculo.
(although I did transfer all the E4 champions over as a reward and are likely grouped together in my Bank). 
