Picking one from each Character I have nicknames done for:

Wily: Type-1 (Type:Null)- Usually shortened to T-1. Wily didn't want his name to basically mean "valueless" and it's a T-1000 reference.

Polly-Gramps(Spiritomb)-Her family 'made' it by assembling the required souls, and the main soul in control is literally one of her ancestors. (A great-great grandfather)

Mahra - Sundae(Alakazam):Because of the spoons and it has a sweet tooth.