1. Mewtwo and Lucas never were assist trophies. They had "trophies" but only ever appeared in gameplay as playable characters.

At this point, the only real rule is Sakurai's own statement that the character must come from a franchise that has its origins in video games (e.g. no Spongebob or Dragon Ball reps).

Joker is a weird case in that his franchise originated from a series of print novels, but the Persona sub-series itself originated as a PS1 game, so he technically abides by the rule.