When I played through FRLG (many moons ago), I used Blastoise and Flareon as my two-mon team. It’s true, Flareon is not as fast as Jolteon (few Pokémon are) nor does he have as high of a special attack stat. But Flareon’s special is workable and his attack is 4 points shy of Dragonite’s. You’re using Blastoise who is more of a defensive Pokémon so a mixed attacker in Flareon could work for you. The only issue is his movepool, but that can be mitigated by the other four Pokémon on your team.
Also, Shadow Ball will help a lot with Agatha.