I've spent way too much time down this particular fanfic rabbit hole, so I guess I'll weigh in. A huge thing I see writers latch onto is the whole 'loving someone you shouldn'tt' conflict, but made a million times weirder because it's a human and a giant alien robot medic. It's never just about the interspecies thing, though that's the obvious layer. It's more about the crushing weight of being the one responsible person on a team of warriors. In a lot of stories, the reader character is this point of fragile, human vulnerability in a war zone, and Ratchet is constantly battling this terror that his medical skills won't be enough to keep them safe. The emotional conflict comes from him trying to maintain professional distance to avoid that paralyzing fear, while simultaneously being drawn in by the very humanity he's trying to protect. He's gruff because caring too much is a liability in his mind.
Another angle I enjoy is when the reader is also a professional—maybe a human engineer or scientist drafted by the Autobots. Then the conflict shifts. It becomes a clash between Ratchet's centuries of Cybertronian experience and the reader's fresh, unconventional human perspective. He's frustrated by what he sees as reckless, short-sighted ideas; the reader is frustrated by his rigidity and dismissal. The emotional core there is a mutual, grudging respect that has to break down walls of pride and tradition. It's less about forbidden love and more about two brilliant minds butting heads until they realize they're looking at the same problem from opposite ends. The romance, when it happens, feels earned because it's built on that foundation of acknowledged competence.
Sometimes the conflict is purely internal for Ratchet, which can be the most compelling to read if done well. He's a soldier who has watched friends die for millennia. Allowing himself to form a deep bond with a creature whose lifespan is a blink to him is portrayed as a special kind of torture. I've read fics where the central tension isn't whether they'll get together, but how Ratchet deals with the inevitable grief he's signing up for. Will he pull away to spare them both? Or will he decide that a short, bright connection is worth the long, lonely aftermath? That's a heavier, more philosophical take that really digs into his character beyond the sarcastic exterior. The emotional payoff is quieter, often just a moment of resigned acceptance rather than a grand declaration.