The "no Legendary rule" technically isn't an official rule, every Legendary encounter so far in the games are not the first Pokémon encountered in the areas they are at (which would be breaking rule two to catch). Victini, contrary to what some believe, is a legit catch as he is the first and only Pokémon to be encountered in Liberty Garden.
Some Fridge Brilliance from Petty's LG and HG runs. In LG Locke had a Graveler named Broseph who died by using Self Destruct. Broseph reappears in the HG run as a Geodude, claiming that when Graveler explode they break apart into several Geodude. Which handily explains why there are so goddamn many of them in the games.
Why is it that the mons tend to be so much closer to (or crave so much more attention from) their trainers in Nuzlockes than normal runs of the games, whether they acknowledge it or not? There are three ways for a Pokémon to lose happiness points: fainting, trading (which resets happiness) and bitter medicine. It's no wonder that the survivors of a Nuzlocke end up with a much higher happiness level than those in runs that 'allow' fainting.
It could also be a sort of selection effect: Only the Pokémon most devoted to their trainers would be willing to put their lives on the line in battle, so those are the ones that actually stay on the team to fight even though they could potentially die.
Squirtle and Charmander's little slap fight at the start of the Fire Red run makes more sense once you've seen their Origin Story.
Team Plasma preaches that Trainers are needlessly brutal to Pokemon for their own glory. The entire point of the Nuzlocke Challenge is to put your Pokemon's very lives on the line every time they battle, for no other purpose but the challenge (i.e., your own glory). Team Plasma is right!
In "White: Hard Mode", Bianca and Cheren are shown to have stalked and harassed poor Hilbert so badly that he's hung himself by the time Ruby gets there. Cheren and Bianca's response boils down to "Oh darn, now we need a new bestie!"—which begs the question: Has this happened before?