I think the most interesting thing about MCU fanfic themes is how they shift with the movies, but some are perennial favorites. Redemption arcs are huge, obviously—Loki, Bucky, Wanda, even Thanos gets them. But lately I've seen way more fics that aren't just about fixing canon, they're about escaping it. Characters get a second chance, they know what's coming, and the story is about dodging the script entirely. It's less 'how do we save Tony' and more 'Tony wakes up in 2008 with all his memories and decides to retire and open a bike shop in Malibu, leaving Fury on read.'
Then there's the 'found family' stuff, but it's gotten messy. It's not just the Avengers as a happy team anymore; post-'Civil War', it's often about fractured groups stitching themselves back together, or about characters forming entirely new, weird little units. Like, I read a series where post-'Endgame', Clint and Nebula start a support group for people who got snapped, and Rocket teaches them woodworking. It's oddly specific, but it fills a niche the movies skipped.
And identity exploration is everywhere, but it's moved past just secret identities. It's about integrating the superhero persona with the person, or losing the powers and having to figure out who you are without them. There's a whole subgenre of 'Tony Stark survives but the arc reactor is gone and he has to deal with being a normal-ish human with PTSD and a billion-dollar company,' and honestly, those are sometimes more compelling than the big battle fics.