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.
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!