Another theory regarding Felicity is that she is the shows take on Oracle, aka Barbara Gordon, and thus her father is Jim Gordon. While there are obvious similarities between the characters, and the show may want to go down the route of Felicity being their version of Oracle (although they may not be able to use the name) theres a lot of rights issues - not least the fact that a young Jim Gordon is appearing on Gotham - that would prevent her from being related to Gordon. Other, more likely theories for who her father is are Martin Stein, the professor who forms one half of Firestorm, or Damien Darhk, set to be the major villain of season 4.