Honestly, I've been knee-deep in this corner of the 'Gundam SEED Destiny' fandom for ages, and the tropes write themselves because of the source material. The most persistent one has to be the 'enemies to reluctant allies to lovers' arc, but it's almost always executed through a shared, isolating grief. They're both pilots who've lost people, and writers love exploring that melancholy connection, having them find a quiet understanding in each other's survivor's guilt that no one else can touch.
Another huge one is the 'fix-it' scenario. The series' ending left a lot of raw feelings for both characters, so fanfic becomes a space to heal that. Marina's pacifism clashing with Setsuna's soldier mindset gets revisited, but instead of ending in ideological deadlock, it becomes a dialogue. You'll see a lot of fics where Setsuna, post-series, seeks out Marina not for battle, but to finally talk about what peace could even look like for someone like him, and Marina has to move beyond her ideals to engage with the messy reality he represents.
Less common but really fascinating are the cross-dimension AUs. I've stumbled upon a few where, say, Marina is a civilian relief worker and Setsuna is a war photographer, or they're both students in a completely mundane setting. It strips away the mobile suits and the war, trying to distill that core dynamic of a gentle idealist and a hardened realist into a different context to see if it still sparks.