In prototype system, there are no classes. Yes, JS has no classes and ES6 classes is just a syntactic sugar, internally JS does prototype-based wiring for you.
Class-based languages are based on a deep-rooted duality of Classes & Object Instances. For instance, if we create an object of the class Vehicle, such as Red Car, and send it a message to deliver super heavy materials, it is not feasible because Red Car is not equipped for that and it is something that's wired in Vehicle class. This highlights the importance of subclassing, which enables creating specialized classes, such as Sports Car and Truck, with their own unique capabilities.
However, predicting the future qualities of objects and classes is challenging, and systems can become rigid when the initial design does not anticipate future changes. And this was one of the motivation to create prototype feature, as such use cases occur in real world development all the time.