Alright, this is a mash-up that shouldn't work but somehow often does, and it usually boils down to how well the writer handles the tech and the scale. The absolute top-tier for me has to be 'Of Sparks and Infinity Stones' over on AO3. It nails the weirdly compatible themes of god-like alien robots and god-like superheroes by focusing on the eternal guardians thing—the Primes and the Asgardians, the AllSpark and the Infinity Stones. The writer treats Cybertronian tech as its own branch of cosmic power, so when Tony Stark gets his hands on a piece of it, the resulting arms race with Megatron feels earned, not just a 'who would win' playground fight. I stumbled on it after binging a bunch of IDW comics, and it just clicked.
Another one that stuck with me was a shorter, less-known series called 'Rust and Vibranium.' It's a post-'Endgame' fix-it where the Autobots arrive on a battered Earth, and it's less about giant robots punching Thanos and more about the societal and technological rebuild. The dynamic between Optimus and Cap, two weary leaders who've lost their worlds, is handled with a quiet respect I really appreciated. The comments section had some great debates about whether an Earth-made Transformer could lift Mjolnir, which is the kind of nerdy depth I live for.
My personal bias leans towards stories where the crossover feels necessary to explore an idea the original can't, not just a cool visual. The best ones make you forget how absurd the premise is after the first chapter.