Maybe make him some huge threat to the world like some eldritch horror. They'd have to change the design but they've already made incomprehensible mons work before with the ultra beasts.
I just feel it would be a really cool callback, maybe give him his own type like the bird type that's weak to and affective against nothing.
A lot of people call giratina the devil but he was just one of Arceus' creations that got banished, missingno could actually be a being that's not supposed to exist.
Just a thought though since he's always been a really cool playground rumour that turned out to be true. Now a days we strip the games bare on release leaving nothing to be discovered through worship of mouth.
Justice for missingno
by dre_the_brazilian