Champions online has a Nemesis system in place where the player gets to create a "Nemesis" that will randomly show up to mess with you. It's a side mission but it was fun you never knew when he would show. Players got to create the look of their villain and choose from a list of henchman and personality traits. I know they have a lot on their plate but down the road it would be cool.
Too bad no matter what personality trait you gave the nemesis, he/she/it would always make that obnoxious death ray. So if STO does this, do it right! Make it more than one storyline possible or don't even bother wasting time.