Thunderbolt is over Flash Cannon on Jirachi because pokemon really isn't a linear game. What I mean by this is that just because you pack an electric move on x pokemon doesn't mean you don't have to put electric move on y pokemon. Flash Cannon / Psychic on Jirachi is less threatening than Thunderbolt / Psychic because the latter has better coverage, and allows Jirachi to set up CMs better. Flash Cannon / Psychic would allow skarmory to phaze you willy nilly, and you honestly wouldn't like that. If you are up against a Gyarados and cant kill it off with Psychic, and it has earthquake, are you going to stop your potential sweep with Jirachi by going to Rotom? If anything, Thunderbolt is a staple on that set and if you feel Flash Cannon would work better than Psychic, you could potentially use it. Thunderbolt helps you so you can threaten a wider variety of pokemon so you can get your sweep up better.