Weirdly enough, I find the most consistent conflict is just... logistics? Like, Reimu's the shrine maiden dealing with youkai incidents, Marisa's a magician who often causes them, and the tension's built right in. Are they friends who happen to be on opposite sides of a professional dynamic, or is there something more that forces them to navigate that line? I've seen a ton of fics where Marisa's latest experiment blows up part of the shrine, and Reimu has to be angry on principle but is secretly relieved it's just Marisa being an idiot and not a real threat. The conflict isn't about hatred, it's about the friction between duty and personal affection, which is way more interesting to me than a simple enemies-to-lovers arc.
Sometimes it gets philosophical, too—Reimu's role as maintainer of balance versus Marisa's pursuit of magical knowledge without regard for boundaries. That's a classic 'order vs. chaos' setup, but in Gensokyo it plays out with tea and danmaku duels instead of epic battles. The resolution often isn't one side winning; it's them finding a new, weird equilibrium that works for their specific, messed-up relationship.
Honestly, the stories where they're just bickering over who ate the last dango feel more real than the high-stakes ones. The domestic spats highlight how comfortable they are, which in itself can be its own low-grade conflict—neither wanting to admit how much they rely on the routine.