I feel like a lot of modern isekai, especially the ones that came after that whole 'overpowered cheat skill' trend, really downplay the sheer, visceral disorientation of being thrown into another world. The early classics in novels or manga, like parts of 'Mushoku Tensei', actually lingered on it—the language barrier being absolute hell, the terror of not knowing local customs, the physical sickness from different food or water. Now, so many stories hand-wave that with an automatic 'comprehension' spell. But even beyond survival, the biggest challenge I see is often psychological integration. Can the protagonist ever truly belong? Or are they forever an observer with cheat codes? They might build a kingdom or have a harem, but there's this underlying loneliness, this feeling of being a tourist in your own life. The ones that grapple with that, where the hero starts forgetting their original world's face or feels guilty for 'replacing' the body's original owner, hit way harder for me than another inventory management scene.
Another subtle challenge that gets overlooked is moral drift. You're plopped into a feudal, monster-infested world with your 21st-century ethics. Do you try to change it? Can you? Or do you slowly adopt its harsher rules to survive? Seeing a character who was once just an office worker reluctantly make a 'kill or be killed' choice, and then having to live with that erosion of their old self, is fascinating. It's less about the dragon attack and more about the quiet dinner afterward where they realize they don't feel as bad as they think they should. That internal conflict is the real meat of a good isekai for me, not just leveling up.