Darkonesfan, your villain reminds me of David Xanatos from Gargoyles, except I don’t think he was ever naive (I dunno…maybe when he was four?).
I could see a couple of FBI agents, not unlike Mulder and Scully, coming to the town to investigate the abnormalities that satellites have been picking up, like the light beacon from the time vortex. (Actually, X-Files meets Storybrook would be a hoot as a crossover fic…I must see if that exists.) They might not necessarily be villains, but would have the potential to really throw a wrench in the works. Of course we’ve already tread some of that path with the Greg and Tamara plotline. Maybe some characters who were actually personable and not shady.
Another character I thought of the other day was more a parody idea: The Keeper of Lost Plot Devices. He keeps a vault (Storybrook is honeycombed with vaults, dontcha know.) containing all the objects and loose ends that seem to have been forgotten about by the characters: Pandora’s box, King George’s vengeance, the fact that there is most likely a Home Office still out there somewhere…and he just releases these items at random from their cages on occasion, so the characters are forced to tie up loose ends.
Hey, there are two X-Files crossovers to be found! Must read now!