Man, that's a deep cut question. Jolteon x Flareon isn't one of the bigger ships in the Pokémon fandom—it's kind of a niche within a niche—but it's got a dedicated following because of the elemental opposition. The most popular theme by far is enemies-to-lovers, playing up the electric/fire type rivalry as a metaphor for clashing personalities. One's fast and sharp-tongued, the other is passionate and maybe a bit stubborn. I've seen a ton of trainer-academy AUs where they're rivals forced to partner up. There's also a surprising amount of hurt/comfort, usually with Flareon getting injured from a rain battle or something and Jolteon, against its own prickly nature, having to provide care.
A less obvious but really cool theme is societal or pack hierarchy stuff. Since Jolteon and Flareon are both evolved Eeveelutions, stories often explore them as 'chosen' paths within an Eevee colony, with their relationship causing tension or bridging divides. I read one ages ago where a Jolteon was the pack's scout and a Flareon was the hearth-keeper, and their slow-burn romance changed how the whole group interacted. The elemental imbalance also leads to a lot of power-dynamic fics, sometimes with a protective edge, other times with a competitive spark that fuels the romance. It's less about grand adventure and more about the small, charged moments between them.
You also get crossover AUs surprisingly often—like a 'Warriors' style feral cat clan setting, or even modern human AUs where their personalities are translated into college students or baristas. The appeal seems to be taking two Pokémon that are visually and thematically distinct and finding the common ground, or making the friction itself the point of attraction. It's a ship built on contrast, so the themes always orbit that idea.